Hello all,
Thanks to Holger and everyone who responded to my last message on the
subject.
I have been trying to implement mm_pbsa and I've come up against a
couple of errors that I
can't seem to overcome. (As an aside, I have a code fix if anyone wants
to use this module with the glycam paramaters for carbohydrates)
My system consists of a protein receptor with 2019 atoms, and a
carbohydrate ligand of 51 atoms (and water).
Using the GC option to get snapshots:
I get the error: broken pipe
and a log file like this:
=>> Reading input parameters
Found PREFIX => Gal1Lac
Found PATH => 01_Snapshots/
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found GC => 1
Found AS => 0
Found DC => 0
Found MM => 0
Found GB => 0
Found PB => 0
Found MS => 0
Found NM => 0
Found DCTYPE => 2
Found IGB => 4
Found SALTCON => 0.00
Found EXTDIEL => 80.0
Found SURFTEN => 0.0072
Found SURFOFF => 0.00
Found DELPHI => /usr/local/programs/delphif77/export/delphi
Found BOX => NO
Found NTOTAL => 2050
Found NSTART => 1
Found NSTOP => 2050
Found NFREQ => 50
Found NUMBER_LIG_GROUPS => 1
Found LSTART => 2020
Found LSTOP => 2070
Found NUMBER_REC_GROUPS => 1
Found RSTART => 1
Found RSTOP => 2019
Found TRAJECTORY =>
/usr/people/mford/Galectin/1.galctn_1_LacNAc_1/6.Carnal/MD_Full_Run.mdcrd.gz
=>> Checking sanity
Checking GENERAL
Checking GC
Checking TRAJ
=>> Creating input
make_crd input
=>> Creating coordinates
Executing makecrd
Something wrong with NGR 2020 2019
I've tried using snapshots from a Carnal coordinate strip of the same
trajectory, but I get nothing but empty all.out files.
Any help is appreciated...
Michael Ford
Received on Thu Oct 10 2002 - 07:23:24 PDT
