On Mon, Nov 8, 2010 at 6:45 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
> You just need to define two Receptor groups. For example:
>
> NUMBER_LIG_GROUPS 1
> LSTART 2622
> LSTOP 3862
> NUMBER_REC_GROUPS 2
> RSTART 1
> RSTOP 262
>
Beware of typos -- this looks like it should be RSTOP 2621, not 262.
> RSTART 3863
> RSTOP 3864
>
> Placing a '2' after NUMBER_REC_GROUPS defines two receptor groups, and then
> you can define the atom numbers associated with the metals using the second
> set of RSTART/RSTOP (I used atoms 3863 and 3864 as a guess since I didn't
> know their respective numbers in your system).
>
> Good luck!
>
> -Bill
>
> On Mon, Nov 8, 2010 at 4:24 AM, xuemeiwang1103 <xuemeiwang1103.163.com
> >wrote:
>
> > Dear All :
> > Recently,I began to calculate the binding free energy by using the
> > MMPBSA meathod.But when I prepared the .prmtop file I meet the
> > problem.Following the MMPBSA tutorial , the script :
> > .........
> > NUMBER_LIG_GROUPS 1
> > LSTART 2622
> > LSTOP 3862
> > NUMBER_REC_GROUPS 1
> > RSTART 1
> > RSTOP 262
> > .............
> > In this script, I kown"RSTART 1 RSTOP 262" means the receptor is from
> > atom 1 to 262. But consedering my system, there are two meatal ions, the
> > protein is from residues 1 to 500, the ligand number is 501, then
> followned
> > two ions(residues 502 and 503). I want to treat the protein and the
> meatal
> > ions as the receptor, How could I deal with this if the number is not
> > consecutive ? Thank you very much!
> >
> >
> >
> > _______________________________________________
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 08 2010 - 08:30:05 PST
