VMD-L Mailing List

From: lloyd riggs (lloyd.riggs_at_gmx.ch)
Date: Fri Sep 28 2012 - 08:49:12 CDT

Dear All,

I have run dozens of large multi protein-small molecules systems in gromacs. I have in the past used vmd as my main visualization tool just to observe traj, and usually use gromacs tools for analysis.

I was interested in using the NAMD energy functions, to cross correlate, and because it allows to pick single atoms, which turns into a pain in gromacs, after you have exhausted your index files. One can do this in gromacs, but it is a pain and often easier to just re-index something and run the saame trajectory again...

in any case,

I have problems as I have gone through all the online steps, and still get an error;

ERROR) Error reading optional structure information from coordinate file XXX.psf
ERROR) Will ignore structure information in this file.

I have tried breaking it up into chuncks and re-assembling it, building small molecules from scratch using the plugins, etc...

any suggestions on how to get a proper .psf file that is readable for a large system (850 aminos) 28 small molecules (1600 Na, K Cl) and 32000 H2O?

my main problems as I can see is it limits solvent total to about 100000, then complains of duplicates, and the small molecules have naming problems, even if I give them all CHARMM , AMBER or X-PLOR name IDS.

SIncerely,

Stephan Watkins