VMD-L Mailing List
From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Tue Sep 25 2007 - 19:00:30 CDT
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- Reply: Dhiraj Srivastava: "Re: topology file in /linux/src/vmd-1.8.6/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp"
- Reply: L. Michel Espinoza-Fonseca: "Re: topology file in /linux/src/vmd-1.8.6/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp"
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Hi All
I was trying to simulate a system with NAD. i am trying to use
topology file /linux/src/vmd-1.8.6
/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp to generate
psf and pdb file. although i am able to generate psf and pdb file using
psfgen with no error but when i am loading pdb and psf file in to vmd, i am
finding a very long, unnatural bond between AC5' and AH5'. although when i
am loading PDB file alone (coming from psfgen), then i am not finding any
problem in the structure.
I tried to use stream file in psfgen but psfgen does not accept this format.
what may be the reason of getting very long bond and how can i fix the
problem?
Thank you
-- Dhiraj K. Srivastava Department of Chemistry University of Missouri-Columbia MO, 65211 Ph. no. 001-573-639-0153
- Next message: Peter Freddolino: "Re: Re: topology file in /linux/src/vmd-1.8.6/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp"
- Previous message: L. Michel Espinoza-Fonseca: "Re: topology file in /linux/src/vmd-1.8.6/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp"
- Next in thread: Dhiraj Srivastava: "Re: topology file in /linux/src/vmd-1.8.6/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp"
- Reply: Dhiraj Srivastava: "Re: topology file in /linux/src/vmd-1.8.6/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp"
- Reply: L. Michel Espinoza-Fonseca: "Re: topology file in /linux/src/vmd-1.8.6/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp"
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