On Sun, Oct 31, 2010 at 6:14 PM, Logan Ahlstrom <logana.email.arizona.edu>wrote:
> I am currently running MMPBSA calculations (with perl scripts) on a
> particular protein-protein interface. However, the “receptor” and “ligand”
> designations I need for this interface are non-consecutive in sequence.
> For
> example, for a complex with 4000 atoms, I want the ligand to be atoms
> 1-1000
> and 2001-3000, and I want to specify the receptor as atoms 1001-2000 and
> 3001-4000. In the input script I want to specify something like the
> following, but I do not know the correct syntax or if it’s even possible:
>
>
>
> BOX NO
>
> NTOTAL 4000
>
> NSTART 1
>
> NSTOP 250
>
> NFREQ 1
>
> #
>
> NUMBER_LIG_GROUPS 1
>
I think this needs to be 2 -- You are specifying 2 groups of ligand atoms.
>
> LSTART 1
>
> LSTOP 1000
>
> LSTART 2001
>
> LSTOP 3000
>
>
>
> NUMBER_REC_GROUPS 1
>
Likewise here.
>
> RSTART 1001
>
> RSTOP 2000
>
> RSTART 3001
>
> RSTOP 4000
>
>
>
> Does anyone have any suggestions? Any input would be helpful.
>
> Sincerely,
>
> Logan S. Ahlstrom
> Department of Chemistry and Biochemistry
> University of Arizona
> _______________________________________________
> 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 Sun Oct 31 2010 - 16:00:02 PDT
