VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 17 2004 - 10:13:00 CST

Luis,
  Can you make us a small DCD file to experiment with?
If so, I don't need a huge file, just something small that I can
use to exercise the dcd plugin.
Perhaps the new version of Charmm has done something different
with fixed atoms compared to prior versions? You might CC your
message to the Charmm developers, since they would likely know
what, if anything, has been changed in the new version and might
have suggestions for how to cope with it.

I've heard from someone else about a recent 64-bit build of Charmm
producing DCD files that VMD/CatDCD can't read, so hopefully we can
bang out a solution to both problems at once if I get enough test files.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 17, 2004 at 01:39:28AM -0500, Luis Gracia wrote:
> Hi!
>
> I am triying to read a dcd with fixed atoms created with charmm, but vmd
> dies when it tries to read it (first I read a pdb with the structure
> info). I have also tried "catdcd -num" and it makes a "Segmentation
> fault". Removing the fixed atoms (CONS...) works perfectly. I thought
> this was supported in the vmd plugins. Any hints?
>
> What am I using?
> - catdcd 3.0 (linux 2.6.4)
> - vmd 1.8.2 (linux 2.6.4)
> - vmd file plugins: latest version (03/05/2004), just downloaded
> - charmm 28b2 in both AIX and IRIX. This is the script for charmm that
> should reproduce the files (pdb and dcd), the only thing you need to
> change is the location of "toppar":
>
> -------------------------------------
> * test
> * LGV'04
> *
>
> LOWER
> BOMBLEVEL -1
> FAST
>
> SET toppar /hosts/miro/homes/luis/toppar
> OPEN UNIT 1 NAME @toppar/top_all22_prot.inp READ CARD
> OPEN UNIT 2 NAME @toppar/par_all22_prot.inp READ CARD
>
> READ RTF UNIT 1 CARD
> READ PARA UNIT 2 CARD
> CLOSE UNIT 1
> CLOSE UNIT 2
>
> READ SEQUENCE CARD
> * test
> *
> 5
> GLY SER HSD MET SER
> GENERATE PROT SETUP
>
> IC SEED 1 N 1 CA 1 C
> IC PARAM
> IC PURGE
> IC BUILD
>
> UPDATE RDIE EPS 4.
> CONS FIX SELE RESID 1 .OR. RESID 2 END
>
> OPEN UNIT 20 NAME test.pdb WRITE CARD
> WRITE COOR PDB UNIT 20
> * test
> *
> CLOSE UNIT 20
>
> OPEN UNIT 30 NAME "test.dcd" WRITE FILE
> DYNA LEAP VERLET NSTEP 10 NPRIN 500 iuncrd 30 -
> IHTFRQ 20 FIRSTT 300. FINALT 1500. TEMINC 50. IASORS 1
> CLOSE UNIT 30
>
> STOP
> ---------------
>
>
> Thanks for the help.
>
> Best,
>
> Luis
>
> --
> Luis Gracia, PhD
> Department of Physiology & Biophysics
> Weill Medical College of Cornell University
> 1300 York Avenue, Box 75
> New York, NY 10021
>
> Tel: (212) 746-6375
> Fax: (212) 746-6361
> lug2002_at_med.cornell.edu 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078