Hello AMBER users,
I have simulated a complex composed of 11 chains and 6 ligand molecules by
using AMBER10 for 10 ns. Now i want to calculate binding energies for
complex with
respective ligands by using mm_pbsa.pl. I am using following input
file for extracting coordinates: (extract_coords.mmpbsa)
PREFIX snapshot
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../complex-vac.prmtop
RECPT ../protein.prmtop
LIGPT ../pvb.prmtop
#
GC 1
AS 0
DC 0
#
MM 0
GB 0
PB 0
MS 0
#
NM 0
#
.MAKECRD
#
BOX YES
NTOTAL 32270
NSTART 1
NSTOP 200
NFREQ 25
#
NUMBER_LIG_GROUPS 6
LSTART 4585
LSTOP 4659
LSTART 4660
LSTOP 4734
LSTART 4735
LSTOP 4809
LSTART 4810
LSTOP 4884
LSTART 4885
LSTOP 4959
LSTART 4960
LSTOP 5034
NUMBER_REC_GROUPS 11
RSTART 1
RSTOP 320
RSTART 321
RSTOP 760
RSTART 761
RSTOP 1076
RSTART 1077
RSTOP 1516
RSTART 1517
RSTOP 1832
RSTART 1833
RSTOP 2294
RSTART 2295
RSTOP 2610
RSTART 2611
RSTOP 3072
RSTART 3073
RSTOP 3388
RSTART 3389
RSTOP 4144
RSTART 4145
RSTOP 4584
#
.TRAJECTORY
TRAJECTORY ./prod4.mdcrd
with this input file, log file is showing an massage that only 10
NUMBER_REC_GROUPS are allowed.
Also what further changes can be advised for calculating mmpbsa energy
for my complex structure having 6 ligands. What about specification of
prmtops in extract_coords.mmpbsa. Here i have specified prmtop for 1st
ligand only. Should i include prmtops for other ligands also (i.e.
pvd.prmtop, pvf.prmtop ...) in LIGPT. I know prmtops are not required
in extraction but will be needed in binding energy calculation.
Regards
*Shaikh Naeem Attari*
Research Scholar
Department of Pharmacoinformatics <
http://pharmacoinformatics.info>
National Institute of Pharmaceutical Education and Research<
http://niper.ac.in>
(NIPER), S.A.S. Nagar, India.
*+91-7814727792*
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Received on Mon Jul 30 2012 - 05:00:03 PDT
