AMBER Archive (2002)

Subject: [Fwd: Re: trouble with snapshots GC option of MM_PBSA]

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Thu Oct 10 2002 - 11:15:39 CDT

Hi Michael,

although you fixed the problem yourself, in general there is a bugfix
for the "Something wrong with NGR ..." case. Have a look at
http://www.amber.ucsf.edu/amber/bugfixes70.html, bugfix.5 .

> I have just fixed my own problem. I set the ligand as atoms 1-2019
> (actually the protein atoms) and the receptor as atoms 2020-2070. I
> hope this will not interfere with later analysis.....
No, I don't see why it should make any problem - receptor and ligand is
just a matter of definition.

Best regards

Holger

>
> Mike Ford
>
> Michael Ford wrote:
> >
> > 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 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
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
+++++++++++++++++++++++++++++++++++++++++++++