Fi
if you have 2 ligand and 2 receptor :
> NTOTAL 4000
>
> NSTART
1
>
> NSTOP 250
>
> NFREQ
1
>
> #
>
> NUMBER_LIG_GROUPS 2
>
> LSTART 1
>
> LSTOP 1000
>
>
LSTART 2001
>
> LSTOP
3000
>
>
>
>
NUMBER_REC_GROUPS 2
>
> RSTART
1001
>
> RSTOP
2000
>
> RSTART
3001
>
> RSTOP 4000
> Date: Sun, 31 Oct 2010 15:14:20 -0700
> From: logana.email.arizona.edu
> To: amber.ambermd.org
> Subject: [AMBER] MMPBSA ligand/receptor selections
>
> 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
>
> LSTART 1
>
> LSTOP 1000
>
> LSTART 2001
>
> LSTOP 3000
>
>
>
> NUMBER_REC_GROUPS 1
>
> 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
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Received on Fri Nov 05 2010 - 05:00:03 PDT
