Dear amber users,
I'm trying to perform the calculation of Energy decomposition per-residue with Amber9. This is part of my input file (the most relevant):
################################################################################
.DECOMP
#
# Energy decomposition parameters (this section is only relevant if DC = 1 above)
#
# Energy decomposition is performed for gasphase energies, desolvation free
# energies calculated with GB, and nonpolar contributions to desolvation
# using the LCPO method.
# For amino acids, decomposition is also performed with respect to backbone
# and sidechain atoms.
#
# DCTYPE - Values of 1 or 2 yield a decomposition on a per-residue basis,
# values of 3 or 4 yield a decomposition on a pairwise per-residue
# basis. For the latter, so far the number of pairs must not
# exceed the number of residues in the molecule considered.
# Values 1 or 3 add 1-4 interactions to bond contributions.
# Values 2 or 4 add 1-4 interactions to either electrostatic or vdW
# contributions.
#
# COMREC - Residues belonging to the receptor molecule IN THE COMPLEX.
# COMLIG - Residues belonging to the ligand molecule IN THE COMPLEX.
# RECRES - Residues in the receptor molecule.
# LIGRES - Residues in the ligand molecule.
# {COM,REC,LIG}PRI - Residues considered for output.
# {REC,LIG}MAP - Residues in the complex which are equivalent to the residues
# in the receptor molecule or the ligand molecule.
#
DCTYPE 2
#
COMREC 1-331
COMLIG 332-332
COMPRI 1-332
RECRES 1-331
RECPRI 1-331
RECMAP 1-331
LIGRES 1-1
LIGPRI 1-1
LIGMAP 332-332
#
################################################################################
In my complex I have a protein binding only one small ligand and I done this job with good results but I worked with the entire protein and I wish do this calculating DC only for certain amino acids residues (in other words I want do it only for aa that mutate from the wild type protein)in order to decrease the computational time. How can I select these residues if it is possible?
More precisely I want perform DC only for 102, 143 and 170 residues of my receptor and, obviously, for my ligand (332).
All advice will be welcome!!!
Many thanks and best regards
-erik-
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Received on Fri Jan 15 2010 - 07:30:03 PST
