VMD-L Mailing List

From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Wed Mar 17 2004 - 00:39:28 CST

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