On 1/7/17 3:24 PM, abhisek Mondal wrote:
So I'm supposed to run "g_dist_mpi", right ? I'm on gromacs-4.6.2.
If you're using an old version, the syntax is totally different, so you will
have to make lots of changes to the script (or not use it at all).
The catch here to analyze the COM distances between 2 pull groups. Am I
getting that right ?
Yes.
-Justin
On Sun, Jan 8, 2017 at 1:46 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/7/17 2:51 PM, abhisek Mondal wrote:
Hi,
I'm pulling ligand out of protein using umbrella sampling method in
gromacs-4.6.2.
Using "trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep" command generated
500 different files (selected "SYSTEM" in interactive prompt, need to
study
protein and ligand simultaneously). But when I use "perl distances.pl"
command I get none of the distances calculated.
Following output was generated:
...
Processing configuration 497...
Processing configuration 498...
Processing configuration 499...
Processing configuration 500...
readline() on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $distance in concatenation (.) or string at
distances.pl line 30.
readline() on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $distance in concatenation (.) or string at
distances.pl line 30.
readline() on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $distance in concatenation (.) or string at
distances.pl line 30.
readline() on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $distance in concatenation (.) or string at
distances.pl line 30.
readline() on closed filehandle IN at distances.pl line 16.
...
Help me out here. What did go wrong ?
gmx distance failed. Run gmx distance yourself and see what the error
message is. The script just executes gmx distance and assumes everything
works because it's designed for a tutorial. You may have to modify it to
get it to work in your system; you can't assume it is plug-and-play.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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