From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 18 2004 - 19:31:16 CST

Luis,
  I've just been debugging this and there is a bug in the VMD
dcd plugin code for reading the fixed atoms, I'm testing it out
now. As it turns out, its not a 32-bit versus 64-bit issue, I
think it is just a simple error in the logic of the dcd reader
plugin. I should have a new DCD plugin that fixes this bug in the
next day or so after I'm done testing.

  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