Topic Options
#3353 - 09/25/04 05:12 PM Syntax to write crd file so that it is viewable in VMD
hlwood Offline

Forum Member

Registered: 09/08/03
Posts: 119
I would suggest writing out pdb and psf files from within charmm. Then you can edit the psf to look like this.....

Code:

PSF

3 !NTITLE
* SETUP OF TEST JOB : CHORISMATE MUTASE W/ 3 PREPHENATES
* H. LEE WOODCOCK 6/15/2001
* DATE: 9/ 7/ 4 17:33: 9 CREATED BY USER: hlwood

14516 !NATOM
1 CMA 1 MET N 56 -0.300000 14.0070 0
2 CMA 1 MET HT1 2 0.330000 1.00800 0
3 CMA 1 MET HT2 2 0.330000 1.00800 0
4 CMA 1 MET HT3 2 0.330000 1.00800 0
5 CMA 1 MET CA 22 0.210000 12.0110 0
6 CMA 1 MET HA 6 0.100000 1.00800 0
7 CMA 1 MET CB 23 -0.180000 12.0110 0
8 CMA 1 MET HB1 3 0.900000E-01 1.00800 0
9 CMA 1 MET HB2 3 0.900000E-01 1.00800 0
10 CMA 1 MET CG 23 -0.140000 12.0110 0



notice... 2 arguments have been deleted from the first line and 2 columns have been deleted from the actual data.

after this run.... vmd -psf file.psf -pdb file.pdb

this works for me, hope it helps.

Top
#3354 - 03/31/05 02:25 PM Re: Syntax to write crd file so that it is viewable in VMD [Re: hlwood]
jmwict13 Offline
Forum Member

Registered: 11/14/03
Posts: 36
Loc: W. Lafayette, IN USA
VMD can actually read standard CHARMM CRD files without editing, starting with version 1.8.2 (current version is 1.8.3). Use the COR plugin instead of CRD to load the molecule.

If this is still an issue for any of you.
_________________________
Joshua Ward Graduate Student Purdue University Department of Medicinal Chemistry and Pharmacology

Top

Moderator:  John Legato, lennart