VMD-L Mailing List

From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Wed Aug 04 2021 - 14:17:11 CDT

Dear all,

I could fix the problem. Looking into the topology file
(toppar_drude_master_protein_2019g.str) I discovered two terminal patches
for N-terminal as follows:
PRES NTER 1.000 ! N-terminus in polypeptide
!
! HT1
! (+) /
! --CA---N--HT2
! | \
! HA HT3
!
DELETE ATOM HN

and

PRES NTES 1.000 ! N-terminus in single amino acid
! Note: with CT3 use NTER
!
! HT1
! (+) /
! --CA---N--HT2
! | \
! HA HT3
!
DELETE ATOM HN

and the same for C-terminal (CTER and CTES). Using NTES and CTES instead of
NTER and CTER in the tcl script fixed the problem..

All the best,
Zeynab

On Wed, Aug 4, 2021 at 1:52 PM zeynab hosseini <hosseinizeynab93_at_gmail.com>
wrote:

> 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
>
>