From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jan 24 2007 - 13:09:04 CST
Hi Neela,
did you try putting the line
BOND NT C
in your PRES entry? This would be the proper way to do it, but I didn't
see that on the list of things you tried.
Peter
Neelanjana Sengupta wrote:
> Hello everyone,
>
> I am trying to use psfgen to create a .psf file for
> AcetylProlineAmide, which is basically { ACP-PRO-NH2 }. I have the
> structure (in .pdb ) for this.
> Now, I am using the 'PRES ACP' from the Charmm topology file without a
> problem. For the 'NH2" patch, I create a ' PRES ACT ' in the topology
> file (a modification to PRES CT2):
>
> PRES ACT 0.00
> ATOM NT NH2 -0.62
> ATOM HT1 H 0.32
> ATOM HT2 H 0.30
> BOND NT HT1 NT HT2
> DONOR HT1 NT
> DONOR HT2 NT
>
> At the bottom of my "RESI PRO", I have:
> PATCHING FIRST ACP LAST ACT
>
> The PROBLEM:
> psfgen skips the 'C-NT' bond, and I get I obtain the (HT1-NT-HT2)
> disjointed form the rest of the molecule. I have tried re-naming the
> 'NT' to 'N', and also tried it the other way, by having the bond {C
> +NT} in the PRO topology.
>
> Could someone please tell me what the solution is?
>
> Thanks a lot,
> Neela
> ****************************************
> Neelanjana Sengupta, PhD student
> Dept. of Chemistry
> Univ. of California-Irvine
> Irvine, CA 92697
> USA
> Phone: 1-949-824 9921
> email: sengupta_at_uci.edu <mailto:sengupta_at_uci.edu>
> ****************************************
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