From: Subramanian Vaitheeswaran (vaithee_at_umd.edu)
Date: Fri Aug 24 2007 - 07:54:41 CDT
Hi Shyamala,
The functional forms of the LJ potential may be different in charmm and xplor. From the charmm parm file:
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
Check whether xplor uses the more conventional form:
V(LJ) = 4 * eps * [(sigma/r)**12 - sigma/r)**6]
S. Vaitheeswaran
(Vaithee)
---- Original message ----
>Date: Thu, 23 Aug 2007 12:09:30 -0700
>From: "shyamala iyer" <shyamala.iyer_at_gmail.com>
>Subject: namd-l: Error bad vdW format in Charmm parameter file
>To: namd-l_at_ks.uiuc.edu
>
> 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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