On 3/19/15 12:28 AM, RINU KHATTRI wrote:
hello everyone
i am unable to understand the result of gmx check .it gives frames and
time values .g_dist is worked in all protein related residues but i
want to calculate the distance between some residues of protein and
ligand for ligand i got same problem like mismatch.
The reason I had you use gmx check was to figure out how many atoms you saved in
the trajectory. If it's fewer than the atom numbers specified in the index
file, you have identified your problem. From your description, it sounds like
you only saved protein coordinates during the run or in some trjconv
post-processing task. You can't analyze something that's not there.
-Justin
kindly help
On Mon, Mar 16, 2015 at 5:02 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 3/16/15 6:43 AM, RINU KHATTRI wrote:
hello everyone
I am working on protein complex with popc membrane gromcs version is 4.5.5
i want to calculate the distance between two residues during the
simulation (200ns) i have been made the .ndx file of atoms of two
residues and concatenate .xtc file and final .tpr file
g_dist -f full.xtc -s final.tpr -n atom.ndx -o dist.xvg
Molecule in topology has atom numbers below and above natoms (3893).
You are probably trying to use a trajectory which does not match the
first 3893 atoms of the run input file.
You can make a matching run input file with tpbconv.
the indx file is having the atom no which are present in last.gro file
kindly help
So what does gmxcheck tell you about the contents of the .tpr and the .xtc?
Likely you have a mismatch in what you saved to the trajectory either in the
run or when using trjconv at some point.
-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
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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