AMBER Archive (2002)

Subject: Re: trouble with snapshots GC option of MM_PBSA

From: Michael Ford (mford_at_ccrc.uga.edu)
Date: Thu Oct 10 2002 - 09:31:05 CDT

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.....

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