From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jan 24 2007 - 18:03:39 CST
Hi Neela,
the C-CA-N-O improper involves the previous residue, and is thus
impossible for a first residue of a segment. The other, however,
probably shouldn't be skipped; you'll need to add an improper to your
patch that has the proper name for the nitrogen (ie, it should be NT -C
CA CD instead of N -C CA CD), or else not change the name of the
nitrogen atom.
The internal coordinates are only used for guessing coordinates for
atoms that aren't there, so they don't hurt, but will have no effect if
you already have all of the atoms present.
Peter
Neelanjana Sengupta wrote:
> 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
> <mailto: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> <mailto:
> 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 <mailto:sengupta_at_uci.edu>
> ****************************************
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