[gmx-users] g_dist

[RINU KHATTRI]

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.
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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