Dear AMBER users,
The ambermd.org website only provide using mmpbsa= calculate the
wild-type protein-ligand delta G.
Is there any tu=rials available for computational alanine scanning using
AMBER9?
I have a copy of mmpbsa.perl from amber 6, I refer to the mm_pbsa.p=n
amber9 version, and added mutation information in the regular .MAKECRD section in the extract_coords.mmpbsa file for amber9, according to the o nline tutorial, please see below,
#
BOX =n=p; YES
NTOTAL &nb=; 28159
NSTART &n=p; =
NSTOP &nb=; 1500000
NFREQ &=sp; 5# to mutate a cys to ala
NUMBER_MUTANT_GROUPS 1
MUTANT_=OM1 578
MUTANT_ATOM2=
MUTANT_KEEP &n=p; 580
MUTANT_REFERENCE&nb=; 575
NUMBER_LIG_GROUPS &nb=; 2
LSTART 32
LSTOP &=sp; 1784
L=ART &nbs= 1785
LSTOP =125
NUMBER_RE=5FGROUPS 1
RSTART =
RSTOP&nb=; 31
then, perl ./mm_pbsa.pl extract_coords.m=bsa > extract_coords.log,
it says,
"Can't use string ("578")= an ARRAY ref while "strict refs" in use at
/opt/scripps/amber9//src/mm=Fpbsa/mm_pbsa_createinput.pm line 462.".
It seems it does not =cognize the mutation info that I put in in the
extract_coord file. Can =y one of you mm_pbsa experts be kind to
reply and help out?
Than=!
Andy
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Received on Sat Jun 06 2009 - 01:10:11 PDT
