VMD-L Mailing List

From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Wed Aug 04 2021 - 16:16:26 CDT

If you look at the parameter file, you will see that for single amino acid, the correct patch is NTES and CTES
________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of zeynab hosseini <hosseinizeynab93_at_gmail.com>
Sent: Wednesday, August 4, 2021 1:06 PM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: psfgen 2.0

Dear all,

I already posted this question but nobody answered. I searched within the forum to check if this issue has been solved before, but unsuccessful. I post it again with the hope that somebody could guide me. Would be very much appreciated..

Here is the question:

I want to do a test run for the molecular dynamics simulation of an amino acid (AA) using Drude polarizable force field (FF). I picked ASP AA (ASP_autopsf.pdb<https://urldefense.com/v3/__https://drive.google.com/file/d/1Z_yT2e2S_JV2cyofpiV619SRMzienhBI/view?usp=sharing__;!!DZ3fjg!pkmnx8MMSQVZbGMgKYBA30oNz_XvNguj_C-pS534IKz1JUV1-5NnRmyoR13rvAF0Ug$>) and used psfgen (vmd-1.9.4a51) to create ASP .psf and .pdb files compatible with Drude FF. Initially, I performed the following script without the terminal patches (first NTER; last CTER) and I noticed that some atoms from the ASP terminals are missing. Then, I added the terminal patches as follows, but the produced .pdb file ( ASP-p.pdb<https://urldefense.com/v3/__https://drive.google.com/file/d/1NRrI727YXb_Xef4U-dS_RRIL0qD9A78g/view?usp=sharing__;!!DZ3fjg!pkmnx8MMSQVZbGMgKYBA30oNz_XvNguj_C-pS534IKz1JUV1-5NnRmyoR10JVpWmLg$> & ASP-p.psf<https://urldefense.com/v3/__https://drive.google.com/file/d/17B3HXdVhxuOeV94I8I03omjfS96jv46y/view?usp=sharing__;!!DZ3fjg!pkmnx8MMSQVZbGMgKYBA30oNz_XvNguj_C-pS534IKz1JUV1-5NnRmyoR139h5dn8Q$>) contains an extra Oxygen atom (and related lone-pair) located at the origin which is far from the ASP itself.
############
package require psfgen
topology drude_toppar_2019/toppar_drude_master_protein_2019g.str
segment AP1 {
pdb ASP_autopsf.pdb
first NTER
last CTER
auto angles dihedrals
}
coordpdb ASP_autopsf.pdb AP1
guesscoord
writepdb ASP-p.pdb<https://urldefense.com/v3/__https://drive.google.com/file/d/1NRrI727YXb_Xef4U-dS_RRIL0qD9A78g/view?usp=sharing__;!!DZ3fjg!pkmnx8MMSQVZbGMgKYBA30oNz_XvNguj_C-pS534IKz1JUV1-5NnRmyoR10JVpWmLg$>
writepsf ASP-p.psf<https://urldefense.com/v3/__https://drive.google.com/file/d/17B3HXdVhxuOeV94I8I03omjfS96jv46y/view?usp=sharing__;!!DZ3fjg!pkmnx8MMSQVZbGMgKYBA30oNz_XvNguj_C-pS534IKz1JUV1-5NnRmyoR139h5dn8Q$>
######################

Here is the output for the script including the terminal patches:
rlwrap: Command not found.
/usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib/x86_64-linux-gnu/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.4a51 (December 21, 2020)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu<mailto:vmd_at_ks.uiuc.edu>
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 8 CPUs detected.
Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 HT
Info) Free system memory: 4988MB (63%)
Info) No CUDA accelerator devices available.
Info) Dynamically loaded 3 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
2.0
psfgen) reading topology file drude_toppar_2019/toppar_drude_master_protein_2019g.str

psfgen) DRUDE master topology and parameter stream file
psfgen) Includes water, 2013
psfgen) Ions updated, June 2018
psfgen) Nucleic acid/carbohydrate/lipid update January 2017
psfgen) Opt molecular ions, fylin 2018
psfgen) Halogen and NBFIX terms, fylin 2018
psfgen) Updated protein FF with opt alpha/Thole, fylin 2018
psfgen)
psfgen) reading topology from stream file
psfgen) Topology for drude water, ions and proteins
psfgen)
psfgen) Created by CHARMM version 41
psfgen) cross-term entries present in topology definitions
psfgen) skipping parameters in stream file
psfgen) Drude polarizable FF parameters
psfgen)
psfgen) building segment AP1
psfgen) reading residues from pdb file ASP_autopsf.pdb
psfgen) extracted 1 residues from pdb file
psfgen) setting patch for first residue to NTER
psfgen) setting patch for last residue to CTER
psfgen) enabling angle autogeneration
psfgen) enabling dihedral autogeneration
Info: generating structure...
psfgen) Info: skipping bond C-N at beginning of segment.
psfgen) Info: skipping improper N-C-CA-HN at beginning of segment.
psfgen) Info: skipping improper C-CA-N-O at beginning of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment--_000_YTBPR01MB31833A645A64170F2A0217D3E6F19YTBPR01MB3183CANP_--