VMD-L Mailing List

From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Wed Aug 04 2021 - 12:06:36 CDT

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
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.
psfgen) Info: skipping conformation CA-C-N-CA at beginning of segment.
psfgen) Info: skipping conformation N-CA-C-O at beginning of segment.
psfgen) Info: skipping conformation N-CA-C-N at beginning of segment.
psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.

segment complete.
psfgen) reading coordinates from pdb file ASP_autopsf.pdb for segment AP1
psfgen) Info: guessing coordinates for 3 atoms (1 non-hydrogen)
psfgen) Info: guessing coordinates for 8 lonepairs
psfgen) Warning: failed to guess coordinates for 3 atoms
psfgen) Info: writing pdb file ASP-p.pdb
psfgen) Info: pdb file complete.
psfgen) Info: writing psf file ASP-p.psf
psfgen) total of 36 atoms
psfgen) total of 10 drude particles
psfgen) total of 4 anisotropy entries
psfgen) total of 8 lone pairs
psfgen) total of 32 bonds
psfgen) total of 24 angles
psfgen) total of 30 dihedrals
psfgen) total of 2 impropers
psfgen) total of 0 explicit exclusions
psfgen) Structure requires EXTended PSF format
psfgen) total of 0 cross-terms
psfgen) Info: psf file complete.
vmd >

########################

The relate lines of .pdb are as following:

###################
REMARK original generated coordinate pdb file
ATOM 1 N ASP A 201 54.031 29.991 188.076 1.00 0.00 AP1
 N
ATOM 2 DN ASP A 201 54.031 29.991 188.076 1.00 0.00 AP1
 N
ATOM 3 HT1 ASP A 201 54.797 30.563 188.371 1.00 0.00 AP1
 H
ATOM 4 HT2 ASP A 201 53.531 29.653 188.874 1.00 0.00 AP1
 H
ATOM 5 HT3 ASP A 201 53.418 30.519 187.488 1.00 0.00 AP1
 H
ATOM 6 CA ASP A 201 54.552 28.848 187.319 1.00 0.00 AP1
 C
ATOM 7 DCA ASP A 201 54.552 28.848 187.319 1.00 0.00 AP1
 C
ATOM 8 HA ASP A 201 55.030 29.254 186.434 1.00 0.00 AP1
 H
ATOM 9 C ASP A 201 53.431 27.920 186.831 1.00 0.00 AP1
 C
ATOM 10 DC ASP A 201 53.431 27.920 186.831 1.00 0.00 AP1
 C

*ATOM 11 O ASP A 201 0.000 0.000 0.000 -1.00 0.00
 AP1 OATOM 12 DO ASP A 201 0.000 0.000 0.000 -1.00 0.00
   AP1 OATOM 13 LPOA ASP A 201 0.000 0.000 0.000 -1.00 0.00
     AP1 HATOM 14 LPOB ASP A 201 0.000 0.000 0.000 -1.00
 0.00 AP1 H*
ATOM 15 OT1 ASP A 201 52.551 28.286 187.132 1.00 0.00 AP1
 O
ATOM 16 DOT1 ASP A 201 52.551 28.286 187.132 1.00 0.00 AP1
 O
ATOM 17 OT2 ASP A 201 53.836 27.160 186.323 1.00 0.00 AP1
 O
ATOM 18 DOT2 ASP A 201 53.836 27.160 186.323 1.00 0.00 AP1
 O
##################

Would you kindly guide me on what is wrong?

All the best,
Zeynab