AMBER Archive (2003)

Subject: Re: MM_PBSA

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Wed Jan 29 2003 - 09:24:58 CST

Dear Martin,

only set RECEPTOR to 1 in the "@GENERAL" part of the mm_pbsa.in file and
then edit the @DECOMP part such as:

@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 0
COMLIG 0
COMPRI 0
RECRES 1-76
RECPRI 1-76
RECMAP 0
LIGRES 0
LIGPRI 0
LIGMAP 0

Best regards

Holger

> Dear AMBER community,
> does anyone know how to specify COMREC, COMPRI, LIGMAP etc. for a
> decomposition mm-pbsa calculation for receptor only? (from receptor
> trajectory) I filled in only REC* fields (COM and LIG either leaving blank
> or putting 0-0) and the error message was #RECMAP + #LIGMAP != COMPRI
>
> Could you please help?
>
> Thanks.
>
> Regards,
>
> Martin
>
> ----------------------------------------------------------------------------
> ----------------------------------------------------------------------------
> ----
> Martin Lepsik, PhD student Phone: +420/2/20183-540, Fax:
> +420/2/20183-292
> Dept. of Theor Chem & Center for Complex molecular Systems and Biomolecules
> Institute of Organic Chemistry and Biochemistry (IOCB)
> Flemingovo nam 2,
> Czech Academy of Sciences,
> 166 10, Prague 6,
> Czech Rep. 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++