AMBER Archive (2002)

Subject: trouble with snapshots GC option of MM_PBSA

From: Michael Ford (mford_at_ccrc.uga.edu)
Date: Thu Oct 10 2002 - 09:23:24 CDT


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