On 1/7/17 3:36 PM, abhisek Mondal wrote:
Alright, I'm trying.
Please tell me one thing, given the fact I want to analyse the
protein-ligand pull scenario, what should be my choice during the prompt i
get after executing "g_dist_mpi -s pull.tpr -f conf200.gro -n index.ndx -o
all"
Reading file pull.tpr, VERSION 4.6.2 (single precision)
Group 0 ( System) has 2648311 elements
Group 1 ( Protein) has 1693 elements
Group 2 ( Protein-H) has 1301 elements
Group 3 ( C-alpha) has 163 elements
Group 4 ( Backbone) has 489 elements
Group 5 ( MainChain) has 653 elements
Group 6 ( MainChain+Cb) has 805 elements
Group 7 ( MainChain+H) has 815 elements
Group 8 ( SideChain) has 878 elements
Group 9 ( SideChain-H) has 648 elements
Group 10 ( Prot-Masses) has 1693 elements
Group 11 ( non-Protein) has 2646618 elements
Group 12 ( Other) has 15 elements
Group 13 ( JZ4) has 15 elements
Group 14 ( NA) has 1602 elements
Group 15 ( CL) has 1608 elements
Group 16 ( Water) has 2643393 elements
Group 17 ( SOL) has 2643393 elements
Group 18 ( non-Water) has 4918 elements
Group 19 (Protein_chain_A) has 3210 elements
Group 20 ( JZ4) has 15 elements
Group 21 ( NA) has 1602 elements
Group 22 ( CL) has 1608 elements
Group 23 ( Water_and_ions) has 2646603 elements
Group 24 ( r_1-163) has 5605 elements
Group 25 ( r_164) has 39 elements
Do I go with System ? I only need to see protein-ligand pull though.
What groups defined your reaction coordinate for the pulling? Those are the
groups you want.
-Justin
Can you give me some suggestions ?
On Sun, Jan 8, 2017 at 1:58 AM, Justin Lemkul <jalem...@vt.edu> wrote:
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
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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
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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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==================================================
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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