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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Received on Sun Apr 23 2006 - 06:07:09 PDT
