================================================================================
= =
= oooooo rrrrrrr aaaaa ccccccc =
= oooooooooo rrrrrrrr aaaaaaaaa ccccccccc =
= ooo ooo rr rrr aaa aaa ccc =
= oo oo rr rr aaa aaa cc =
= oo oo rr rrr aaaaaaaaaaa cc =
= ooo ooo rr rrr aaaaaaaaaaa ccc =
= oooooooooo rr rr aa aa ccccccccc =
= oooooo rr rrr aa aa ccccccc =
= =
= (Version 4.0.1) =
= =
= "A Molecular Dynamics Program to Simulate Complex Molecular Systems" =
= =
= Copyright(C) 1989 - 1997 =
= =
= All Right Reserved =
= =
= =
= =
= =
= ORAC is provided "as is" and without any warranty express or implied. =
= The user assumes all risks of using ORAC. =
= =
= The user may make copies of ORAC for his/her own use, and modify those =
= copies. The user MAY NOT distribute any copy of the original or =
= modified source code to any users at any sites other than his/her own. =
= =
= =
= =
= =
= =
= Centre d'Etudes Saclay =
= Gif sur Yvette, FRANCE =
= =
= =
= =
= =
= =
= =
================================================================================
=========================== INPUT TO THE RUN ===================================
= =
=############################################################### =
=# Minimize Crystallographic structure form PDBank =
=############################################################### =
= =
=# =
=# Set MD cell and read pdb coordinates =
=# =
=&SETUP =
= CRYSTAL 50.0 50.0 50.0 90.0 90.0 90.0 =
= READ_PDB ../pdb/bpti0.pdb =
=&END =
= =
=# =
=# read ASCII databases and build up solute =
=# =
=&PARAMETERS =
= READ_TPG_ASCII ../lib/amber95.tpg =
= READ_PRM_ASCII ../lib/amber95.prm =
= ADD_TPG SOLUTE =
= bond 1sg 2sg residue 5 55 =
= bond 1sg 2sg residue 14 38 =
= bond 1sg 2sg residue 30 51 =
= END =
= JOIN SOLUTE =
= arg-h pro asp phe cys leu glu pro pro tyr thr gly pro =
= cys lys ala arg ile ile arg tyr phe tyr asn ala lys =
= ala gly leu cys gln thr phe val tyr gly gly cys arg =
= ala lys arg asn asn phe lys ser ala glu asp cys met =
= arg thr cys gly gly ala-o po4 hoh x 167 =
= END =
=&END =
= =
=# =
=# Simulation Commands: Minimize the structure =
=# =
=# =
=&SIMULATION =
= MINIMIZE =
= CG 0.01 =
= END =
=&END =
= =
=# =
=# Cutoff for minimize is 7.0 A. =
=# =
=&POTENTIAL =
= UPDATE 20.0 1.5 =
= CUTOFF 7.0 =
= STRETCHING =
= QQ-FUDGE 0.83333 =
= LJ-FUDGE 0.50 =
=&END =
= =
=# =
=# do 20 minimization step and intermediate printout every 5 =
=# =
=&RUN =
= CONTROL 0 =
= TIME 20.0 =
= PRINT 5.0 =
=&END =
= =
=# =
=# write final pdb file to 1.pdb =
=# =
=&INOUT =
= ASCII 20.0 OPEN 1.pdb =
=&END =
= =
================================================================================
Checking Input ...... ---->
* * * W A R N I N G * * *
PROPERTY(&RUN) is O or less than TIMESTEP(&VARIABLES); NPROP set to 1000
********* W A R N I N G W A R N I N G ************
* 1 ERRORS WHILE EXECUTING VERIFY_INPUT
******** Recoverable Error Program Continues ******
========================================================================
= =
= SOLUTE: Assembling Molecules =
= =
========================================================================
SOLUTE: Linking the molecule together ---->
SOLUTE: Adding extra links ---->
SOLUTE: Searching for Bonds ---->
SOLUTE: Searching for Bendings ---->
SOLUTE: Searching for Bendings to Omit ---->
SOLUTE: Assigning a Type to Each Atom ---->
SOLUTE: Find All Possible 1-4 Interactions ---->
SOLUTE: Searching for Bond Parameters ---->
SOLUTE: Searching for Bendings Parameters ---->
SOLUTE: Pick rigid fragments that Match Input ---->
SOLUTE: Add extra P-Torsions ---->
SOLUTE: Match P-Torsions with Parameters ---->
SOLUTE: Pick I-Torsions that Match Input ---->
SOLUTE: Add extra I-Torsions ---->
SOLUTE: Match I-Torsions with Parameters ---->
************************************************************************
* SOLUTE: Initial TOPOLOGY List *
* *
* 1398 Atoms 1244 Bonds 1244 FLexible Bonds *
* 0 Rigid Bonds 1799 Angles 2732 P-Torsions *
* 199 I-Torsions 2347 1-4 Inter. *
* *
************************************************************************
Found Charge 6.00000 on Solute Molecule 1
Found Charge -3.00000 on Solute Molecule 2
These parameters are not compatible :
i 1 0.00000 0.00000
j 54 2.00000 0.11000
* * * E R R O R * * *
Wrong Format in 14 LJ parameter file
These parameters are not compatible :
i 1 0.00000 0.00000
j 55 2.00000 0.11000
These parameters are not compatible :
i 1 0.00000 0.00000
j 56 2.00000 0.11000
These parameters are not compatible :
i 1 0.00000 0.00000
j 57 1.32000 0.02200
.... and many other error like these..
========================================================================
= =
= Setting up the Simulation Box =
= =
========================================================================
==========================================
= Reading System Coordinates =
==========================================
Reading the PDB file ---->
PDB file parsed: 1398 atoms; - 772 hydrogens to be assigned
Solute Center of Mass coordinates at
28.546 9.649 0.354
************************************************************************
* New TOPOLOGY List *
* *
* 0 Solvent Mol 0 Atoms Each 169 Solute Mol. *
* *
* For the Sysyem *
* *
* 1398 Atoms 1244 Bonds 1244 FLexible Bonds *
* 0 Rigid Bonds 1799 Angles 2732 P-Torsions *
* 199 I-Torsions 2347 1-4 Inter. *
* *
************************************************************************
********************************************************************************
* *
* I n p u t O p e r a t i o n s C o m p l e t e d *
* *
* I n p u t O p e r a t i o n s C o m p l e t e d *
* *
* *
********************************************************************************
*******************************************************************************
* *
* Minimization for an aggregate composed of 1398 atoms *
* Minimization for an aggregate composed of 1398 atoms *
* Minimization for an aggregate composed of 1398 atoms *
* *
*******************************************************************************
============== P A R A M E T E R S F O R T H E R U N =================
The Minimization will be run from scratch.
Initial atomic coordinates will be generated.
Reject = 0 Steps Run = 20 Steps
Maxrun = 0 Steps
Save Subaverages every 1000 Steps
Save Restart file every 0 Steps
Save PLOT file every 0 Steps
Save PDB file every 20 Steps
Save DUMP file every 0 Steps
potential truncation distance = 7.0000 ang
time-step = 1.0000E+00 fs.
Number of atoms = 1398
CO-matrix
25.00000 0.00000 0.00000
0.00000 25.00000 0.00000
0.00000 0.00000 25.00000
Volume = 125000.000 Ang**3
----------------------------- Neighbor List ------------------------------------
UPDATE every 20 Steps
Dispersion+Electrostatics rspcut = 8.50
************************************************************************
* System TOPOLOGY List *
* *
* 1398 Atoms 1244 Bonds 1244 FLexible Bonds *
* 0 Rigid Bonds 1799 Angles 2732 P-Torsions *
* 199 I-Torsions 2347 1-4 Inter. 524 Atomic Groups *
* 226 Units 169 Molecules *
* *
************************************************************************
================================================================================
********************************************************************************
* *
* I n t e r m e d i a t e R e s u l t s *
* *
* I n t e r m e d i a t e R e s u l t s *
* *
* *
********************************************************************************
Neighbor Lists Dimensions *neighbor( 18459)*
CPUtime for update = 0.030
***************************************
* Not yet at minimum !! *
* GradMax 0.69843E+06 *
***************************************
Tstep = 5.000 Total = 57126.724 TotPot = 57126.724
Coulomb = -7652.840 NonBond = 403.263 Ener14 = 10117.494
Bonded = 56723.462 Stretch = 45011.605 Angle = 9592.190
I-Tors = 25.776 P-Tors = 2093.891 TotTemp = 0.000
ResTemp = 0.000 TraTemp = 0.000
***************************************
* GradMax 0.26772E+01 *
***************************************
Tstep = 10.000 Total = -3787.220 TotPot = -3787.220
Coulomb = -8853.156 NonBond = -7784.520 Ener14 = 9909.408
Bonded = 3997.301 Stretch = 440.460 Angle = 1458.502
I-Tors = 61.854 P-Tors = 2036.484 TotTemp = 0.000
ResTemp = 0.000 TraTemp = 0.000
***************************************
* GradMax 0.93677E-01 *
***************************************
Tstep = 15.000 Total = -8170.596 TotPot = -8170.596
Coulomb = -11344.386 NonBond = -11368.233 Ener14 = 9629.103
Bonded = 3197.638 Stretch = 332.359 Angle = 935.345
I-Tors = 101.311 P-Tors = 1828.623 TotTemp = 0.000
ResTemp = 0.000 TraTemp = 0.000
***************************************
* GradMax 0.40184E-01 *
***************************************
Tstep = 20.000 Total = -10481.638 TotPot = -10481.638
Coulomb = -13032.542 NonBond = -13275.800 Ener14 = 9445.498
Bonded = 2794.163 Stretch = 294.359 Angle = 835.734
I-Tors = 76.857 P-Tors = 1587.213 TotTemp = 0.000
ResTemp = 0.000 TraTemp = 0.000
***************************************
* GradMax 0.30852E-01 *
***************************************
***************************************
* *
* M I N I M I Z A T I O N *
* *
* F I N A L R E S U L T S *
* *
***************************************
Tstep = 20.000 Total = -10481.638 TotPot = -10481.638
Coulomb = -13032.542 NonBond = -13275.800 Ener14 = 9445.498
Bonded = 2794.163 Stretch = 294.359 Angle = 835.734
I-Tors = 76.857 P-Tors = 1587.213 TotTemp = 0.000
ResTemp = 0.000 TraTemp = 0.000
***************************************
* GradMax 0.29430E-01 *
***************************************
===========================================
Total cpu time for the run = 11.840
Total elapsed time for the run = 0.000
Averaged time per step = 0.592
Averaged elapsed per step = 0.000
===========================================
************************************************************************
* *
* PROGRAM COMPLETED *
* *
************************************************************************
|--------------------------------------------------------------|
| ``They're unfriendly. Which is fortunate really; |
| they'd be difficult to love.'' |
| . . . Avon Blake's Seven |
| |
|--------------------------------------------------------------|
================================================================================
= =
= oooooo rrrrrrr aaaaa ccccccc =
= oooooooooo rrrrrrrr aaaaaaaaa ccccccccc =
= ooo ooo rr rrr aaa aaa ccc =
= oo oo rr rr aaa aaa cc =
= oo oo rr rrr aaaaaaaaaaa cc =
= ooo ooo rr rrr aaaaaaaaaaa ccc =
= oooooooooo rr rr aa aa ccccccccc =
= oooooo rr rrr aa aa ccccccc =
= =
= (Version 4.0.1) =
= =
= "A Molecular Dynamics Program to Simulate Complex Molecular Systems" =
= =
= Copyright(C) 1989 - 1997 =
= =
= All Right Reserved =
= =
= =
= =
= =
= ORAC is provided "as is" and without any warranty express or implied. =
= The user assumes all risks of using ORAC. =
= =
= The user may make copies of ORAC for his/her own use, and modify those =
= copies. The user MAY NOT distribute any copy of the original or =
= modified source code to any users at any sites other than his/her own. =
= =
= =
= =
= =
= =
= Centre d'Etudes Saclay =
= Gif sur Yvette, FRANCE =
= =
= =
= =
= =
= =
= =
================================================================================
=========================== INPUT TO THE RUN ===================================
= =
=############################################################### =
=# Minimize Crystallographic structure form PDBank =
=############################################################### =
= =
=# =
=# Set MD cell and read pdb coordinates =
=# =
=&SETUP =
= CRYSTAL 50.0 50.0 50.0 90.0 90.0 90.0 =
= READ_PDB ../pdb/bpti0.pdb =
=&END =
= =
=# =
=# read ASCII databases and build up solute =
=# =
=&PARAMETERS =
= READ_TPG_ASCII ../lib/amber95.tpg =
= READ_PRM_ASCII ../lib/amber95.prm =
= ADD_TPG SOLUTE =
= bond 1sg 2sg residue 5 55 =
= bond 1sg 2sg residue 14 38 =
= bond 1sg 2sg residue 30 51 =
= END =
= JOIN SOLUTE =
= arg-h pro asp phe cys leu glu pro pro tyr thr gly pro =
= cys lys ala arg ile ile arg tyr phe tyr asn ala lys =
= ala gly leu cys gln thr phe val tyr gly gly cys arg =
= ala lys arg asn asn phe lys ser ala glu asp cys met =
= arg thr cys gly gly ala-o po4 hoh x 167 =
= END =
=&END =
= =
=# =
=# Simulation Commands: Minimize the structure =
=# =
=# =
=&SIMULATION =
= MINIMIZE =
= CG 0.01 =
= END =
=&END =
= =
=# =
=# Cutoff for minimize is 7.0 A. =
=# =
=&POTENTIAL =
= UPDATE 20.0 1.5 =
= CUTOFF 7.0 =
= STRETCHING =
= QQ-FUDGE 0.83333 =
= LJ-FUDGE 0.50 =
=&END =
= =
=# =
=# do 20 minimization step and intermediate printout every 5 =
=# =
=&RUN =
= CONTROL 0 =
= TIME 20.0 =
= PRINT 5.0 =
=&END =
= =
=# =
=# write final pdb file to 1.pdb =
=# =
=&INOUT =
= ASCII 20.0 OPEN 1.pdb =
=&END =
= =
================================================================================
Checking Input ...... ---->
* * * W A R N I N G * * *
PROPERTY(&RUN) is O or less than TIMESTEP(&VARIABLES); NPROP set to 1000
********* W A R N I N G W A R N I N G ************
* 1 ERRORS WHILE EXECUTING VERIFY_INPUT
******** Recoverable Error Program Continues ******
========================================================================
= =
= SOLUTE: Assembling Molecules =
= =
========================================================================
SOLUTE: Linking the molecule together ---->
SOLUTE: Adding extra links ---->
SOLUTE: Searching for Bonds ---->
SOLUTE: Searching for Bendings ---->
SOLUTE: Searching for Bendings to Omit ---->
SOLUTE: Assigning a Type to Each Atom ---->
SOLUTE: Find All Possible 1-4 Interactions ---->
SOLUTE: Searching for Bond Parameters ---->
SOLUTE: Searching for Bendings Parameters ---->
SOLUTE: Pick rigid fragments that Match Input ---->
SOLUTE: Add extra P-Torsions ---->
SOLUTE: Match P-Torsions with Parameters ---->
SOLUTE: Pick I-Torsions that Match Input ---->
SOLUTE: Add extra I-Torsions ---->
SOLUTE: Match I-Torsions with Parameters ---->
************************************************************************
* SOLUTE: Initial TOPOLOGY List *
* *
* 1398 Atoms 1244 Bonds 1244 FLexible Bonds *
* 0 Rigid Bonds 1799 Angles 2732 P-Torsions *
* 199 I-Torsions 2347 1-4 Inter. *
* *
************************************************************************
Found Charge 6.00000 on Solute Molecule 1
Found Charge -3.00000 on Solute Molecule 2
These parameters are not compatible :
i 1 0.00000 0.00000
j 54 2.00000 0.11000
* * * E R R O R * * *
Wrong Format in 14 LJ parameter file
These parameters are not compatible :
i 1 0.00000 0.00000
j 55 2.00000 0.11000
These parameters are not compatible :
i 1 0.00000 0.00000
j 56 2.00000 0.11000
These parameters are not compatible :
i 1 0.00000 0.00000
j 57 1.32000 0.02200
.... and many other error like these..
========================================================================
= =
= Setting up the Simulation Box =
= =
========================================================================
==========================================
= Reading System Coordinates =
==========================================
Reading the PDB file ---->
PDB file parsed: 1398 atoms; - 772 hydrogens to be assigned
Solute Center of Mass coordinates at
28.546 9.649 0.354
************************************************************************
* New TOPOLOGY List *
* *
* 0 Solvent Mol 0 Atoms Each 169 Solute Mol. *
* *
* For the Sysyem *
* *
* 1398 Atoms 1244 Bonds 1244 FLexible Bonds *
* 0 Rigid Bonds 1799 Angles 2732 P-Torsions *
* 199 I-Torsions 2347 1-4 Inter. *
* *
************************************************************************
********************************************************************************
* *
* I n p u t O p e r a t i o n s C o m p l e t e d *
* *
* I n p u t O p e r a t i o n s C o m p l e t e d *
* *
* *
********************************************************************************
*******************************************************************************
* *
* Minimization for an aggregate composed of 1398 atoms *
* Minimization for an aggregate composed of 1398 atoms *
* Minimization for an aggregate composed of 1398 atoms *
* *
*******************************************************************************
============== P A R A M E T E R S F O R T H E R U N =================
The Minimization will be run from scratch.
Initial atomic coordinates will be generated.
Reject = 0 Steps Run = 20 Steps
Maxrun = 0 Steps
Save Subaverages every 1000 Steps
Save Restart file every 0 Steps
Save PLOT file every 0 Steps
Save PDB file every 20 Steps
Save DUMP file every 0 Steps
potential truncation distance = 7.0000 ang
time-step = 1.0000E+00 fs.
Number of atoms = 1398
CO-matrix
25.00000 0.00000 0.00000
0.00000 25.00000 0.00000
0.00000 0.00000 25.00000
Volume = 125000.000 Ang**3
----------------------------- Neighbor List ------------------------------------
UPDATE every 20 Steps
Dispersion+Electrostatics rspcut = 8.50
************************************************************************
* System TOPOLOGY List *
* *
* 1398 Atoms 1244 Bonds 1244 FLexible Bonds *
* 0 Rigid Bonds 1799 Angles 2732 P-Torsions *
* 199 I-Torsions 2347 1-4 Inter. 524 Atomic Groups *
* 226 Units 169 Molecules *
* *
************************************************************************
================================================================================
********************************************************************************
* *
* I n t e r m e d i a t e R e s u l t s *
* *
* I n t e r m e d i a t e R e s u l t s *
* *
* *
********************************************************************************
Neighbor Lists Dimensions *neighbor( 18459)*
CPUtime for update = 0.030
***************************************
* Not yet at minimum !! *
* GradMax 0.69843E+06 *
***************************************
Tstep = 5.000 Total = 57126.724 TotPot = 57126.724
Coulomb = -7652.840 NonBond = 403.263 Ener14 = 10117.494
Bonded = 56723.462 Stretch = 45011.605 Angle = 9592.190
I-Tors = 25.776 P-Tors = 2093.891 TotTemp = 0.000
ResTemp = 0.000 TraTemp = 0.000
***************************************
* GradMax 0.26772E+01 *
***************************************
Tstep = 10.000 Total = -3787.220 TotPot = -3787.220
Coulomb = -8853.156 NonBond = -7784.520 Ener14 = 9909.408
Bonded = 3997.301 Stretch = 440.460 Angle = 1458.502
I-Tors = 61.854 P-Tors = 2036.484 TotTemp = 0.000
ResTemp = 0.000 TraTemp = 0.000
***************************************
* GradMax 0.93677E-01 *
***************************************
Tstep = 15.000 Total = -8170.596 TotPot = -8170.596
Coulomb = -11344.386 NonBond = -11368.233 Ener14 = 9629.103
Bonded = 3197.638 Stretch = 332.359 Angle = 935.345
I-Tors = 101.311 P-Tors = 1828.623 TotTemp = 0.000
ResTemp = 0.000 TraTemp = 0.000
***************************************
* GradMax 0.40184E-01 *
***************************************
Tstep = 20.000 Total = -10481.638 TotPot = -10481.638
Coulomb = -13032.542 NonBond = -13275.800 Ener14 = 9445.498
Bonded = 2794.163 Stretch = 294.359 Angle = 835.734
I-Tors = 76.857 P-Tors = 1587.213 TotTemp = 0.000
ResTemp = 0.000 TraTemp = 0.000
***************************************
* GradMax 0.30852E-01 *
***************************************
***************************************
* *
* M I N I M I Z A T I O N *
* *
* F I N A L R E S U L T S *
* *
***************************************
Tstep = 20.000 Total = -10481.638 TotPot = -10481.638
Coulomb = -13032.542 NonBond = -13275.800 Ener14 = 9445.498
Bonded = 2794.163 Stretch = 294.359 Angle = 835.734
I-Tors = 76.857 P-Tors = 1587.213 TotTemp = 0.000
ResTemp = 0.000 TraTemp = 0.000
***************************************
* GradMax 0.29430E-01 *
***************************************
===========================================
Total cpu time for the run = 11.880
Total elapsed time for the run = 0.000
Averaged time per step = 0.594
Averaged elapsed per step = 0.000
===========================================
************************************************************************
* *
* PROGRAM COMPLETED *
* *
************************************************************************
|--------------------------------------------------------------|
| ``They're unfriendly. Which is fortunate really; |
| they'd be difficult to love.'' |
| . . . Avon Blake's Seven |
| |
|--------------------------------------------------------------|
================================================================================
= =
= oooooo rrrrrrr aaaaa ccccccc =
= oooooooooo rrrrrrrr aaaaaaaaa ccccccccc =
= ooo ooo rr rrr aaa aaa ccc =
= oo oo rr rr aaa aaa cc =
= oo oo rr rrr aaaaaaaaaaa cc =
= ooo ooo rr rrr aaaaaaaaaaa ccc =
= oooooooooo rr rr aa aa ccccccccc =
= oooooo rr rrr aa aa ccccccc =
= =
= (Version 4.0.1) =
= =
= "A Molecular Dynamics Program to Simulate Complex Molecular Systems" =
= =
= Copyright(C) 1989 - 1997 =
= =
= All Right Reserved =
= =
= =
= =
= =
= ORAC is provided "as is" and without any warranty express or implied. =
= The user assumes all risks of using ORAC. =
= =
= The user may make copies of ORAC for his/her own use, and modify those =
= copies. The user MAY NOT distribute any copy of the original or =
= modified source code to any users at any sites other than his/her own. =
= =
= =
= =
= =
= =
= Centre d'Etudes Saclay =
= Gif sur Yvette, FRANCE =
= =
= =
= =
= =
= =
= =
================================================================================
=========================== INPUT TO THE RUN ===================================
= =
=############################################################### =
=# Minimize Crystallographic structure form PDBank =
=############################################################### =
= =
=# =
=# Set MD cell and read pdb coordinates =
=# =
=&SETUP =
= CRYSTAL 50.0 50.0 50.0 90.0 90.0 90.0 =
= READ_PDB ../pdb/bpti0.pdb =
=&END =
= =
=# =
=# read ASCII databases and build up solute =
=# =
=&PARAMETERS =
= READ_TPG_ASCII ../lib/amber95.tpg =
= READ_PRM_ASCII ../lib/amber95.prm =
= ADD_TPG SOLUTE =
= bond 1sg 2sg residue 5 55 =
= bond 1sg 2sg residue 14 38 =
= bond 1sg 2sg residue 30 51 =
= END =
= JOIN SOLUTE =
= arg-h pro asp phe cys leu glu pro pro tyr thr gly pro =
= cys lys ala arg ile ile arg tyr phe tyr asn ala lys =
= ala gly leu cys gln thr phe val tyr gly gly cys arg =
= ala lys arg asn asn phe lys ser ala glu asp cys met =
= arg thr cys gly gly ala-o po4 hoh x 167 =
= END =
=&END =
= =
=# =
=# Simulation Commands: Minimize the structure =
=# =
=# =
=&SIMULATION =
= MINIMIZE =
= CG 0.01 =
= END =
=&END =
= =
=# =
=# Cutoff for minimize is 7.0 A. =
=# =
=&POTENTIAL =
= UPDATE 20.0 1.5 =
= CUTOFF 7.0 =
= STRETCHING =
= QQ-FUDGE 0.83333 =
= LJ-FUDGE 0.50 =
=&END =
= =
=# =
=# do 20 minimization step and intermediate printout every 5 =
=# =
=&RUN =
= CONTROL 0 =
= TIME 20.0 =
= PRINT 5.0 =
=&END =
= =
=# =
=# write final pdb file to 1.pdb =
=# =
=&INOUT =
= ASCII 20.0 OPEN 1.pdb =
=&END =
= =
================================================================================
Checking Input ...... ---->
* * * W A R N I N G * * *
PROPERTY(&RUN) is O or less than TIMESTEP(&VARIABLES); NPROP set to 1000
********* W A R N I N G W A R N I N G ************
* 1 ERRORS WHILE EXECUTING VERIFY_INPUT
******** Recoverable Error Program Continues ******
========================================================================
= =
= SOLUTE: Assembling Molecules =
= =
========================================================================
SOLUTE: Linking the molecule together ---->
SOLUTE: Adding extra links ---->
SOLUTE: Searching for Bonds ---->
SOLUTE: Searching for Bendings ---->
SOLUTE: Searching for Bendings to Omit ---->
SOLUTE: Assigning a Type to Each Atom ---->
SOLUTE: Find All Possible 1-4 Interactions ---->
SOLUTE: Searching for Bond Parameters ---->
SOLUTE: Searching for Bendings Parameters ---->
SOLUTE: Pick rigid fragments that Match Input ---->
SOLUTE: Add extra P-Torsions ---->
SOLUTE: Match P-Torsions with Parameters ---->
SOLUTE: Pick I-Torsions that Match Input ---->
SOLUTE: Add extra I-Torsions ---->
SOLUTE: Match I-Torsions with Parameters ---->
************************************************************************
* SOLUTE: Initial TOPOLOGY List *
* *
* 1398 Atoms 1244 Bonds 1244 FLexible Bonds *
* 0 Rigid Bonds 1799 Angles 2732 P-Torsions *
* 199 I-Torsions 2347 1-4 Inter. *
* *
************************************************************************
Found Charge 6.00000 on Solute Molecule 1
Found Charge -3.00000 on Solute Molecule 2
These parameters are not compatible :
i 1 0.00000 0.00000
j 54 2.00000 0.11000
* * * E R R O R * * *
Wrong Format in 14 LJ parameter file
These parameters are not compatible :
i 1 0.00000 0.00000
j 55 2.00000 0.11000
These parameters are not compatible :
i 1 0.00000 0.00000
j 56 2.00000 0.11000
These parameters are not compatible :
i 1 0.00000 0.00000
j 57 1.32000 0.02200
.... and many other error like these..
========================================================================
= =
= Setting up the Simulation Box =
= =
========================================================================
==========================================
= Reading System Coordinates =
==========================================
Reading the PDB file ---->
PDB file parsed: 1398 atoms; - 772 hydrogens to be assigned
Solute Center of Mass coordinates at
28.546 9.649 0.354
************************************************************************
* New TOPOLOGY List *
* *
* 0 Solvent Mol 0 Atoms Each 169 Solute Mol. *
* *
* For the Sysyem *
* *
* 1398 Atoms 1244 Bonds 1244 FLexible Bonds *
* 0 Rigid Bonds 1799 Angles 2732 P-Torsions *
* 199 I-Torsions 2347 1-4 Inter. *
* *
************************************************************************
********************************************************************************
* *
* I n p u t O p e r a t i o n s C o m p l e t e d *
* *
* I n p u t O p e r a t i o n s C o m p l e t e d *
* *
* *
********************************************************************************
*******************************************************************************
* *
* Minimization for an aggregate composed of 1398 atoms *
* Minimization for an aggregate composed of 1398 atoms *
* Minimization for an aggregate composed of 1398 atoms *
* *
*******************************************************************************
============== P A R A M E T E R S F O R T H E R U N =================
The Minimization will be run from scratch.
Initial atomic coordinates will be generated.
Reject = 0 Steps Run = 20 Steps
Maxrun = 0 Steps
Save Subaverages every 1000 Steps
Save Restart file every 0 Steps
Save PLOT file every 0 Steps
Save PDB file every 20 Steps
Save DUMP file every 0 Steps
potential truncation distance = 7.0000 ang
time-step = 1.0000E+00 fs.
Number of atoms = 1398
CO-matrix
25.00000 0.00000 0.00000
0.00000 25.00000 0.00000
0.00000 0.00000 25.00000
Volume = 125000.000 Ang**3
----------------------------- Neighbor List ------------------------------------
UPDATE every 20 Steps
Dispersion+Electrostatics rspcut = 8.50
************************************************************************
* System TOPOLOGY List *
* *
* 1398 Atoms 1244 Bonds 1244 FLexible Bonds *
* 0 Rigid Bonds 1799 Angles 2732 P-Torsions *
* 199 I-Torsions 2347 1-4 Inter. 524 Atomic Groups *
* 226 Units 169 Molecules *
* *
************************************************************************
================================================================================
********************************************************************************
* *
* I n t e r m e d i a t e R e s u l t s *
* *
* I n t e r m e d i a t e R e s u l t s *
* *
* *
********************************************************************************
Neighbor Lists Dimensions *neighbor( 18459)*
CPUtime for update = 0.030
***************************************
* Not yet at minimum !! *
* GradMax 0.69843E+06 *
***************************************
Tstep = 5.000 Total = 57126.724 TotPot = 57126.724
Coulomb = -7652.840 NonBond = 403.263 Ener14 = 10117.494
Bonded = 56723.462 Stretch = 45011.605 Angle = 9592.190
I-Tors = 25.776 P-Tors = 2093.891 TotTemp = 0.000
ResTemp = 0.000 TraTemp = 0.000
***************************************
* GradMax 0.26772E+01 *
***************************************
Tstep = 10.000 Total = -3787.220 TotPot = -3787.220
Coulomb = -8853.156 NonBond = -7784.520 Ener14 = 9909.408
Bonded = 3997.301 Stretch = 440.460 Angle = 1458.502
I-Tors = 61.854 P-Tors = 2036.484 TotTemp = 0.000
ResTemp = 0.000 TraTemp = 0.000
***************************************
* GradMax 0.93677E-01 *
***************************************
Tstep = 15.000 Total = -8170.596 TotPot = -8170.596
Coulomb = -11344.386 NonBond = -11368.233 Ener14 = 9629.103
Bonded = 3197.638 Stretch = 332.359 Angle = 935.345
I-Tors = 101.311 P-Tors = 1828.623 TotTemp = 0.000
ResTemp = 0.000 TraTemp = 0.000
***************************************
* GradMax 0.40184E-01 *
***************************************
Tstep = 20.000 Total = -10481.638 TotPot = -10481.638
Coulomb = -13032.542 NonBond = -13275.800 Ener14 = 9445.498
Bonded = 2794.163 Stretch = 294.359 Angle = 835.734
I-Tors = 76.857 P-Tors = 1587.213 TotTemp = 0.000
ResTemp = 0.000 TraTemp = 0.000
***************************************
* GradMax 0.30852E-01 *
***************************************
***************************************
* *
* M I N I M I Z A T I O N *
* *
* F I N A L R E S U L T S *
* *
***************************************
Tstep = 20.000 Total = -10481.638 TotPot = -10481.638
Coulomb = -13032.542 NonBond = -13275.800 Ener14 = 9445.498
Bonded = 2794.163 Stretch = 294.359 Angle = 835.734
I-Tors = 76.857 P-Tors = 1587.213 TotTemp = 0.000
ResTemp = 0.000 TraTemp = 0.000
***************************************
* GradMax 0.29430E-01 *
***************************************
===========================================
Total cpu time for the run = 11.880
Total elapsed time for the run = 0.000
Averaged time per step = 0.594
Averaged elapsed per step = 0.000
===========================================
************************************************************************
* *
* PROGRAM COMPLETED *
* *
************************************************************************
|--------------------------------------------------------------|
| ``They're unfriendly. Which is fortunate really; |
| they'd be difficult to love.'' |
| . . . Avon Blake's Seven |
| |
|--------------------------------------------------------------|
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