VMD-L Mailing List

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Tue Jun 09 2009 - 11:33:41 CDT

Dear All,

in VMD, I need to mess around with some atom ordering for a pdb file
used by another program.

In particular, my CTER patch on the chain's last residue is at the
*beginning* of that residue's definition, but I need to have it at the
*end*.

So I have

ATOM 111 C GLU C 105 79.976 48.485 35.426 1.00 0.00
C C
ATOM 112 OT1 GLU C 105 80.960 48.382 35.575 0.00 0.00
C O
ATOM 113 OT2 GLU C 105 79.124 48.696 35.906 0.00 0.00
C O
ATOM 114 N GLU C 105 80.860 47.914 33.180 1.00 0.00
C N
ATOM 115 HN GLU C 105 81.520 47.355 33.674 0.00 0.00
C H
....

but it should be

ATOM 111 N GLU C 105 80.860 47.914 33.180 1.00 0.00
C N
ATOM 112 HN GLU C 105 81.520 47.355 33.674 0.00 0.00
C H
ATOM 113 CA GLU C 105 79.665 48.228 33.940 1.00 0.00
C C
...
ATOM 139 C GLU C 105 79.976 48.485 35.426 1.00 0.00
C C
ATOM 140 OT1 GLU C 105 80.960 48.382 35.575 0.00 0.00
C O
ATOM 141 OT2 GLU C 105 79.124 48.696 35.906 0.00 0.00
C O

Is there a way I can set this in the topology file psfgen uses?

Thank you,
Sebastian