From: shyamala iyer (shyamala.iyer_at_gmail.com)
Date: Thu Aug 23 2007 - 14:09:30 CDT
Hi,
I am trying to do molecular dynamics on a protein-water-ligand system.
Before trying dynamics with the ligand, I used just the protein and water
system, the charmm topology and parameter files to generate a psf file and
then run namd. That simulation worked fine.
Now, since there was no readymade charmm type topology and parameter file
for the ligand ( a small druG), I used the ProGrg server to get CNS/XPLOR
topology and parameter files for the ligand. To format these files into a
charmm "like" format, I wrote some scripts to get the topology and parameter
files present the info similar to how it is presented in charmm files. The
topology file for the ligand worked, since I was able to use the psfgen and
solvate modules to get my ptotein-ligand complex in a box of water. I
complex looks fine when I loaded the final psf and pdb files in vmd.
But, I am having some trouble with the ligand parameter file. The charmm
topology file has a section for lennard jones potential, but the ligand file
(orig cns/xplor) paramter file does not have a similar section. I however
used a script to change the rest of the ligand parameter file to resemble
the information listed in charmm par files. WHen I run NAMD simulation, I
get this error:
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: BAD vdW FORMAT IN CHARMM PARAMETER FILE
*INE=*tolerance 0.5
Charm++ fatal error:
FATAL ERROR: BAD vdW FORMAT IN CHARMM PARAMETER FILE
*INE=*tolerance 0.5
Abort (core dumped)
I would really appreciate it if someone could help me solve this error.
I have pasted the modified ligand parameter file below.
Thanks,
Shyamala Iyer
!
!
! This file was generated by PRODRG version 061128.0522
! PRODRG written/copyrighted by Daan van Aalten
! and Alexander Schuettelkopf
!
! Questions/comments to dava_at_davapc1.bioch.dundee.ac.uk
!
! When using this software in a publication, cite:
! A. W. Schuettelkopf and D. M. F. van Aalten (2004).
! PRODRG - a tool for high-throughput crystallography
! of protein-ligand complexes.
! Acta Crystallogr. D60, 1355--1363.
!
!
! *** NOTE *** IF YOU USE MORE THAN ONE PRODRG-GENERATED TOPOLOGY IN CNS,
! PLEASE CAREFULLY READ THE FAQ AS THIS MAY CAUSE PROBLEMS
!
!
!set echo=off message=on end
BOND CV42 OV41 12000 1.430
BOND OV41 CV40 18000 1.360
BOND CV40 OV36 24000 1.230
BOND CV40 CV35 16000 1.530
BOND CV35 CV37 16000 1.530
BOND CV35 NV34 18000 1.470
BOND CV37 CV39 16000 1.530
BOND CV37 CV38 16000 1.530
BOND NV34 HVAG 17900 1.000
BOND NV34 CV32 20000 1.330
BOND CV32 OV33 24000 1.230
BOND CV32 CV28 16000 1.530
BOND CV28 CV29 16000 1.530
BOND CV28 NV27 18000 1.470
BOND CV29 CV31 16000 1.530
BOND CV29 CV30 16000 1.530
BOND NV27 HVAF 17900 1.000
BOND NV27 CV25 20000 1.330
BOND CV25 OV26 24000 1.230
BOND CV25 CV23 16000 1.530
BOND CV23 CV24 16000 1.530
BOND CV23 NV22 18000 1.470
BOND NV22 CV19 18000 1.470
BOND NV22 HVAD 17900 1.000
BOND NV22 CV21 18000 1.470
BOND CV19 CV11 16000 1.530
BOND CV21 CV20 16000 1.530
BOND CV20 CV9 16000 1.530
BOND CV9 CV7 16000 1.530
BOND CV9 CV10 20000 1.390
BOND CV7 CV8 16000 1.530
BOND CV7 NV6 18000 1.470
BOND NV6 HVAE 17900 1.000
BOND NV6 CV4 20000 1.330
BOND CV4 OV5 24000 1.230
BOND CV4 CV2 16000 1.530
BOND CV2 CV3 16000 1.530
BOND CV2 NV1 18000 1.470
BOND NV1 HVAB 17900 1.000
BOND NV1 HVAC 17900 1.000
BOND NV1 HVAA 17900 1.000
BOND CV10 CV11 16000 1.530
BOND CV11 CV12 16000 1.530
BOND CV12 CV13 16000 1.530
BOND CV13 CV14 20000 1.390
BOND CV13 CV18 20000 1.390
BOND CV14 CV15 20000 1.390
BOND CV15 CV16 20000 1.390
BOND CV16 CV17 20000 1.390
BOND CV17 CV18 20000 1.390
ANGLE CV42 OV41 CV40 640 109.500
ANGLE OV41 CV40 OV36 800 120.000
ANGLE OV41 CV40 CV35 800 120.000
ANGLE OV36 CV40 CV35 960 121.000
ANGLE CV40 CV35 CV37 880 109.500
ANGLE CV40 CV35 NV34 880 109.500
ANGLE CV37 CV35 NV34 880 109.500
ANGLE CV35 CV37 CV39 880 111.000
ANGLE CV35 CV37 CV38 880 111.000
ANGLE CV39 CV37 CV38 880 111.000
ANGLE CV35 NV34 HVAG 720 115.000
ANGLE CV35 NV34 CV32 960 122.000
ANGLE HVAG NV34 CV32 560 123.000
ANGLE NV34 CV32 OV33 960 124.000
ANGLE NV34 CV32 CV28 960 115.000
ANGLE OV33 CV32 CV28 960 121.000
ANGLE CV32 CV28 CV29 880 109.500
ANGLE CV32 CV28 NV27 880 109.500
ANGLE CV29 CV28 NV27 880 109.500
ANGLE CV28 CV29 CV31 880 111.000
ANGLE CV28 CV29 CV30 880 111.000
ANGLE CV31 CV29 CV30 880 111.000
ANGLE CV28 NV27 HVAF 720 115.000
ANGLE CV28 NV27 CV25 960 122.000
ANGLE HVAF NV27 CV25 560 123.000
ANGLE NV27 CV25 OV26 960 124.000
ANGLE NV27 CV25 CV23 960 115.000
ANGLE OV26 CV25 CV23 960 121.000
ANGLE CV25 CV23 CV24 880 109.500
ANGLE CV25 CV23 NV22 880 109.500
ANGLE CV24 CV23 NV22 880 109.500
ANGLE CV23 NV22 CV19 720 109.500
ANGLE CV23 NV22 HVAD 720 109.500
ANGLE CV23 NV22 CV21 720 109.500
ANGLE CV19 NV22 HVAD 720 109.500
ANGLE CV19 NV22 CV21 720 109.500
ANGLE HVAD NV22 CV21 720 109.500
ANGLE NV22 CV19 CV11 880 109.500
ANGLE NV22 CV21 CV20 880 109.500
ANGLE CV21 CV20 CV9 880 111.000
ANGLE CV20 CV9 CV7 800 120.000
ANGLE CV20 CV9 CV10 800 126.000
ANGLE CV7 CV9 CV10 800 120.000
ANGLE CV9 CV7 CV8 880 109.500
ANGLE CV9 CV7 NV6 880 109.500
ANGLE CV8 CV7 NV6 880 109.500
ANGLE CV7 NV6 HVAE 720 115.000
ANGLE CV7 NV6 CV4 960 122.000
ANGLE HVAE NV6 CV4 560 123.000
ANGLE NV6 CV4 OV5 960 124.000
ANGLE NV6 CV4 CV2 960 115.000
ANGLE OV5 CV4 CV2 960 121.000
ANGLE CV4 CV2 CV3 880 109.500
ANGLE CV4 CV2 NV1 880 109.500
ANGLE CV3 CV2 NV1 880 109.500
ANGLE CV2 NV1 HVAB 720 109.500
ANGLE CV2 NV1 HVAC 720 109.500
ANGLE CV2 NV1 HVAA 720 109.500
ANGLE HVAB NV1 HVAC 640 109.500
ANGLE HVAB NV1 HVAA 640 109.500
ANGLE HVAC NV1 HVAA 640 109.500
ANGLE CV9 CV10 CV11 800 126.000
ANGLE CV19 CV11 CV10 880 109.500
ANGLE CV19 CV11 CV12 880 109.500
ANGLE CV10 CV11 CV12 880 109.500
ANGLE CV11 CV12 CV13 880 111.000
ANGLE CV12 CV13 CV14 800 120.000
ANGLE CV12 CV13 CV18 800 120.000
ANGLE CV14 CV13 CV18 800 120.000
ANGLE CV13 CV14 CV15 800 120.000
ANGLE CV14 CV15 CV16 800 120.000
ANGLE CV15 CV16 CV17 800 120.000
ANGLE CV16 CV17 CV18 800 120.000
ANGLE CV13 CV18 CV17 800 120.000
IMPR CV40 OV41 CV35 OV36 800 0 0.000
IMPR NV34 CV35 HVAG CV32 800 0 0.000
IMPR CV32 NV34 CV28 OV33 800 0 0.000
IMPR NV27 CV28 HVAF CV25 800 0 0.000
IMPR CV25 NV27 CV23 OV26 800 0 0.000
IMPR CV9 CV10 CV7 CV20 800 0 0.000
IMPR NV6 CV7 HVAE CV4 800 0 0.000
IMPR CV4 NV6 CV2 OV5 800 0 0.000
IMPR CV13 CV18 CV14 CV12 800 0 0.000
IMPR CV35 CV40 CV37 NV34 400 0 35.264
IMPR CV37 CV35 CV39 CV38 400 0 35.264
IMPR CV28 CV32 CV29 NV27 400 0 35.264
IMPR CV29 CV28 CV31 CV30 400 0 35.264
IMPR CV23 CV25 CV24 NV22 400 0 35.264
IMPR NV22 CV23 CV19 HVAD 400 0 35.264
IMPR CV7 CV9 CV8 NV6 400 0 35.264
IMPR CV2 CV4 CV3 NV1 400 0 35.264
IMPR NV1 CV2 HVAC HVAB 400 0 35.264
IMPR CV11 CV19 CV12 CV10 400 0 35.264
IMPR CV13 CV14 CV15 CV16 800 0 0.000
IMPR CV14 CV15 CV16 CV17 800 0 0.000
IMPR CV15 CV16 CV17 CV18 800 0 0.000
IMPR CV16 CV17 CV18 CV13 800 0 0.000
IMPR CV17 CV18 CV13 CV14 800 0 0.000
IMPR CV18 CV13 CV14 CV15 800 0 0.000
DIHE CV42 OV41 CV40 CV35 160 2 180.000
DIHE NV34 CV35 CV40 OV41 0 6 0.000
DIHE CV38 CV37 CV35 CV40 19 3 0.000
DIHE CV40 CV35 NV34 CV32 0 6 180.000
DIHE CV28 CV32 NV34 CV35 640 2 180.000
DIHE NV27 CV28 CV32 NV34 0 6 0.000
DIHE CV30 CV29 CV28 CV32 19 3 0.000
DIHE CV32 CV28 NV27 CV25 0 6 180.000
DIHE CV23 CV25 NV27 CV28 640 2 180.000
DIHE NV22 CV23 CV25 NV27 0 6 0.000
DIHE CV25 CV23 NV22 CV21 8 3 0.000
DIHE CV11 CV19 NV22 CV23 8 3 0.000
DIHE CV20 CV21 NV22 CV23 8 3 0.000
DIHE NV22 CV19 CV11 CV12 19 3 0.000
DIHE CV9 CV20 CV21 NV22 19 3 0.000
DIHE CV10 CV9 CV20 CV21 0 6 0.000
DIHE CV20 CV9 CV7 NV6 0 6 0.000
DIHE CV20 CV9 CV10 CV11 1000 2 180.000
DIHE CV9 CV7 NV6 CV4 0 6 180.000
DIHE CV2 CV4 NV6 CV7 640 2 180.000
DIHE NV1 CV2 CV4 NV6 0 6 0.000
DIHE CV4 CV2 NV1 HVAA 8 3 0.000
DIHE CV9 CV10 CV11 CV12 0 6 0.000
DIHE CV13 CV12 CV11 CV19 19 3 0.000
DIHE CV18 CV13 CV12 CV11 0 6 0.000
!NBONds
tolerance 0.5
nbxmod 5
wmin 1.5
repel 1.0
rexponent 4
irexponent 1
rconst 16.0
ctonnb 5.5
ctofnb 6.0
cutnb 7.0
!END
NONBONDED CV42 0.10000 3.29633 0.10000 3.02906
NONBONDED OV41 0.10000 2.58361 0.10000 2.31634
NONBONDED CV40 0.10000 3.29633 0.10000 3.02906
NONBONDED OV36 0.10000 2.58361 0.10000 2.31634
NONBONDED CV35 0.10000 3.29633 0.10000 3.02906
NONBONDED CV37 0.10000 3.29633 0.10000 3.02906
NONBONDED CV39 0.10000 3.29633 0.10000 3.02906
NONBONDED CV38 0.10000 3.29633 0.10000 3.02906
NONBONDED NV34 0.10000 2.67270 0.10000 2.40543
NONBONDED HVAG 0.10000 1.42544 0.10000 1.15817
NONBONDED CV32 0.10000 3.29633 0.10000 3.02906
NONBONDED OV33 0.10000 2.58361 0.10000 2.31634
NONBONDED CV28 0.10000 3.29633 0.10000 3.02906
NONBONDED CV29 0.10000 3.29633 0.10000 3.02906
NONBONDED CV31 0.10000 3.29633 0.10000 3.02906
NONBONDED CV30 0.10000 3.29633 0.10000 3.02906
NONBONDED NV27 0.10000 2.67270 0.10000 2.40543
NONBONDED HVAF 0.10000 1.42544 0.10000 1.15817
NONBONDED CV25 0.10000 3.29633 0.10000 3.02906
NONBONDED OV26 0.10000 2.58361 0.10000 2.31634
NONBONDED CV23 0.10000 3.29633 0.10000 3.02906
NONBONDED CV24 0.10000 3.29633 0.10000 3.02906
NONBONDED NV22 0.10000 2.67270 0.10000 2.40543
NONBONDED CV19 0.10000 3.29633 0.10000 3.02906
NONBONDED HVAD 0.10000 1.42544 0.10000 1.15817
NONBONDED CV21 0.10000 3.29633 0.10000 3.02906
NONBONDED CV20 0.10000 3.29633 0.10000 3.02906
NONBONDED CV9 0.10000 3.29633 0.10000 3.02906
NONBONDED CV7 0.10000 3.29633 0.10000 3.02906
NONBONDED CV8 0.10000 3.29633 0.10000 3.02906
NONBONDED NV6 0.10000 2.67270 0.10000 2.40543
NONBONDED HVAE 0.10000 1.42544 0.10000 1.15817
NONBONDED CV4 0.10000 3.29633 0.10000 3.02906
NONBONDED OV5 0.10000 2.58361 0.10000 2.31634
NONBONDED CV2 0.10000 3.29633 0.10000 3.02906
NONBONDED CV3 0.10000 3.29633 0.10000 3.02906
NONBONDED NV1 0.10000 2.67270 0.10000 2.40543
NONBONDED HVAB 0.10000 1.42544 0.10000 1.15817
NONBONDED HVAC 0.10000 1.42544 0.10000 1.15817
NONBONDED HVAA 0.10000 1.42544 0.10000 1.15817
NONBONDED CV10 0.10000 3.29633 0.10000 3.02906
NONBONDED CV11 0.10000 3.29633 0.10000 3.02906
NONBONDED CV12 0.10000 3.29633 0.10000 3.02906
NONBONDED CV13 0.10000 3.29633 0.10000 3.02906
NONBONDED CV14 0.10000 3.29633 0.10000 3.02906
NONBONDED CV15 0.10000 3.29633 0.10000 3.02906
NONBONDED CV16 0.10000 3.29633 0.10000 3.02906
NONBONDED CV17 0.10000 3.29633 0.10000 3.02906
NONBONDED CV18 0.10000 3.29633 0.10000 3.02906
!set echo=on message=on end
END
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