[gmx-users] g_dist

[Justin Lemkul]

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 <jalemkul at 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
>>
>> jalemkul at 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================