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 Sun Oct 31 2010 - 15:30:02 PDT
