From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Wed Jan 24 2007 - 15:50:09 CST
Hello!
That worked. Thanks
However, I am concerned that it is skipping the impropers and conformations
that arise between the ACP and PRO:
--------
Info: skipping improper C-CA-N-O at beginning of segment.
Info: skipping improper N-C-CA-CD at beginning of segment.
Info: skipping conformation CA-C-N-CA at beginning of segment.
Info: skipping conformation N-CA-C-O at beginning of segment.
Info: skipping conformation N-CA-C-N at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-CD at beginning of segment.
---------
I shoudl have mentioned this before, but do you have any idea what I could
do about this?
Also, since I am using a structure that has already been minimized (and we
actually want to see whether this particular structure is stable ina
simulation), should I not omit the Internal Coordinates (IC) section of ACP
and PRO?
Thanks again,
Neela
On 1/24/07, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
> 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>
> > ****************************************
>
-- **************************************** 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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