VMD-L Mailing List

From: hl332_at_drexel.edu
Date: Tue Mar 06 2007 - 11:38:08 CST

Hi all,
      I have worked with vmd for a few months and never encountered this kind of thing in any pdb. One of the pdb I am using now has unusual residue names for several of them. One of them is as below: instead of PHE, it has APHE and BPHE where every atom coordinates have been given two times:

ATOM 191 CA PHE B --furtherdata
ATOM 192 C PHE B --furtherdate
ATOM 193 O PHE B "
ATOM 194 CB PHE B "
ATOM 195 CG APHE B
ATOM 196 CG BPHE B
ATOM 197 CD1APHE B
ATOM 199 CD2BPHE B
ATOM 202 CE1BPHE B
ATOM 203 CE2BPHE B
ATOM 204 CE2APHE B
ATOM 205 CZ APHE B "
ATOM 206 CZ BPHE B

it shows two benzene rings of PHE residue in vmd as each atom in that ring has been provided two coordinates. PSFGEN confuses this and makes some other structure (generates correctly only half of residue).

 One of the solution i think is to manually edit which i guess is not wise. Please let me know if there is better solution(I am sure it does)

Regards
harish

-------------------------------------------------
Harish Vashisth (Ph.D Candidate)
CAT-361,Chemical & Biological Engg.
Drexel University, Philadelphia, PA
office: 215-895-5823