VMD-L Mailing List

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Thu Oct 20 2005 - 11:41:43 CDT

 It looks like you're attempting to acetylate an ATP with residue ID
number 1. Is this what you want to do? I think the ACE patch is intended
for non-proline amino acid N-termini, but you could patch anything with
an atom type "N" and "HN" in principle, but the bonding may not end up
being what you intended. If you just want to patch an N-terminus, you
probably just need to change your segment identification in the patch
statement to point to a polypeptide, but can't say for sure without
seeing your script & input files...

Christopher H. Chang, Ph.D.
Research Associate
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007

> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu
> [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Per Jr. Greisen
> Sent: Thursday, October 20, 2005 8:36 AM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: Warning: add bond failed in patch ACE
>
> Hey all,
>
> Warning: add bond failed in patch ACE
> no atom N in residue ATP:1 of segment A
> Warning: add improper failed in patch ACE no atom N in
> residue ATP:1 of segment A
> Warning: add improper failed in patch ACE no atom N in
> residue ATP:1 of segment A
>
> I get this message trying to model a complex generating the
> psf. Do I have to change my pdb file and if so (look at the
> atoms in topology file and
> convert???)
>
> Cheers
>
>
> --
> Best Regards
>
> Per Jr. Greisen
> +4528648657
>
>