AMBER Archive (2006)

Subject: AMBER: mm_pbsa: "Missing values for MM ..."

From: Sam (samuel.arey_at_epfl.ch)
Date: Fri Apr 21 2006 - 08:39:19 CDT

Hi,

On attempts to use mm_pbsa, I consistently receive the error statement:

"Missing values for MM BGAS"
or
"Missing values for MM ELE"

depending on my choices for input options.

In an effort to isolate the problem, I have stripped down both the
system and
the mm_pbsa input file options to be as minimalist and "standard" as
possible,
just to see if I can get anything to work. Nonetheless the same error
persists.

In previous posts it has been suggested that either non-standard
residues or the
unintended presence of solvent could produce this kind of error. Although I
would eventually like to treat non-standard residues, in simple test
cases I have
ensured that neither solvent (water, ions) nor non-standard residues are
present.
Additionally, both sander and the ambpdb utility have been applied to my
prmtop
file(s) without any problems.

I have found the lines of code in the mm_pbsa_statistics.pm script that are
responsible for producing the error line. I did not figure out what this
could
be really traced to, given my inputs.

Any advice on what to pursue to track this error?

A sample input file (for a very simple case) is below.

thank you-
Sam

@GENERAL
PREFIX bam_pbsa
PATH ./

COMPLEX 0
RECEPTOR 1
LIGAND 0

RECPT ./bam_strand2_dna.top

GC 0
AS 0
DC 0

MM 1
GB 0
PB 0
MS 0

NM 0

@MM

DIELC 1.0

@MAKECRD

BOX YES
NTOTAL 315
NSTART 1
NSTOP 10
NFREQ 1
NUMBER_LIG_GROUPS 0
LSTART 0
LSTOP 0
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 315

@TRAJECTORY

TRAJECTORY ./dat/bam_dna_first11.crd

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