VMD-L Mailing List

From: simao.pereira_at_di3.units.it
Date: Fri Aug 17 2012 - 09:26:43 CDT

Hi Anki,

Regarding the "Molecule destroyed by Fatal error" check if the format of your .psf file is correct (PSF<http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node21.html>).
Maybe you are missing some atom keywork (resname, segname) depending on the way got the .psf file.

Best,
Simão

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of AnkiReddy katha
Sent: 17 August 2012 13:37
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: multiple residues with same resid and problem with solvation using VMD

Dear VMD users

I got a polymer structure built from Materials Studio and prepared the LAMMPS input data. [cross linked polymer, which contains several monomers ]

Using this LAMMPS input data (atom style : full), i created pdb and psf files using TopoTools.

In these pdb/psf files, multiple resides have same residue number [resid]. [ it would have been good to have one residue ID for each monomer]

When i am trying to solvate this polymer using VMD, it produces an error "Molecule destroyed by Fatal error", i think this could be because of multiple residues having the same resid..

Could you please suggest if i can change the residue numbers [reassign residue numbers starting from 1, so that each residue can have unique ID] using some procedure..

one thing i tried using the commands from Axel's website shown below. However this did not result in any change in the residue numbering. I assume that VMD generates its own numbers for residue IDs starting from "0"
set resid {}
foreach r [$selc get residue] { incr r; lappend resid $r }
$selc set resid $resid

Thank you
best regards
Anki

 Please find here part of the PDB file i am working on, here the residue ID "2" is repeated. Like this there are several residues with "2", "5" ....

CRYST1 108.838 108.838 108.838 90.00 90.00 90.00 P 1 1
ATOM 1 H MEM B 1 16.995 26.512 11.607 0.00 0.00 BULK
ATOM 2 C MEM B 1 15.790 25.078 10.485 0.00 0.00 BULK
ATOM 3 H MEM B 1 15.648 24.384 11.334 0.00 0.00 BULK
ATOM 4 C MEM B 1 15.373 24.703 9.210 0.00 0.00 BULK
ATOM 5 C MEM B 1 15.658 25.568 8.155 0.00 0.00 BULK
ATOM 6 H MEM B 1 15.304 25.276 7.154 0.00 0.00 BULK
ATOM 7 C MEM B 1 16.233 26.830 8.307 0.00 0.00 BULK
ATOM 8 C MEM B 1 16.716 27.141 9.575 0.00 0.00 BULK
ATOM 9 H MEM B 1 17.237 28.087 9.800 0.00 0.00 BULK
ATOM 10 C MEM B 1 16.520 26.266 10.641 0.00 0.00 BULK
ATOM 11 N MEM B 1 14.776 23.475 8.901 0.00 0.00 BULK
ATOM 12 H MEM B 1 15.415 22.712 8.639 0.00 0.00 BULK
ATOM 13 H MEM B 1 13.998 22.960 9.316 0.00 0.00 BULK
ATOM 14 N MEM B 1 16.273 27.690 7.185 0.00 0.00 BULK
ATOM 15 H MEM B 1 15.604 27.287 6.508 0.00 0.00 BULK
ATOM 16 H MEM B 2 31.909 19.495 19.943 0.00 0.00 BULK
ATOM 17 C MEM B 2 32.878 17.587 19.858 0.00 0.00 BULK
ATOM 18 H MEM B 2 33.231 17.824 20.865 0.00 0.00 BULK
..............................................................................
..........................................................................
..........................................................................

ATOM 170 H MEM B 2 27.909 17.166 6.377 0.00 0.00 BULK
ATOM 171 C MEM B 2 27.958 15.740 8.032 0.00 0.00 BULK
ATOM 172 H MEM B 2 28.343 16.471 8.759 0.00 0.00 BULK
ATOM 173 C MEM B 2 27.645 14.460 8.504 0.00 0.00 BULK
ATOM 174 C MEM B 2 27.042 13.585 7.551 0.00 0.00 BULK
ATOM 175 H MEM B 2 26.774 12.572 7.900 0.00 0.00 BULK
ATOM 176 C MEM B 2 26.739 13.945 6.205 0.00 0.00 BULK

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