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?
> _______________________________________________
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> 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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Received on Mon Mar 21 2011 - 05:00:03 PDT
