modified patch to PROline

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Wed Jan 24 2007 - 12:25:21 CST

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
****************************************

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