Thank you so much!
On Mon, Mar 21, 2011 at 5:00 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> You need to set up two different receptor groups, instead of just the one,
> so it should look something like this.
>
> NUMBER_REC_GROUPS 2
> RSTART 1
> RSTOP 190
> RSTART 227
> RSTOP 828
>
> Hopefully that will work better for you.
>
> -Bill
>
> On Mon, Mar 21, 2011 at 7:25 AM, N.R. Jena <nrjena.gmail.com> wrote:
>
> > Hi All,
> > I am calculating PB energies of a DNA having a sequence, say
> > (GTAXCTC)2 by using amber-9 and MMPBSA.pl script. Here X is a modified
> > nucleotide. I can extract snapshots for ligand
> > (here it is X). However, I have problem in extracting snapshots for
> > receptor. The receptor here will be (GTA+CTC i.e. GTACTC)2. My problem
> > is as X is not situated at the end of DNA, I can
> >
> > not create snapshots for(GTACTC)2.My MM-PBSA script is
> > -------------------------------------
> > NUMBER_REC_GROUPS 1
> > RSTART 1
> > RSTOP 190,227-828
> > -------------------------------------
> >
> > In the above script 1-190 refers to GTA while 227-828 refers to CTC.
> > The script is only taking 1-190 as the receptor and leaves 227-828.
> > Will any body suggest me how to define the receptor here in the script?
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Mar 21 2011 - 05:00:04 PDT
