[gmx-users] Calculate RMSD for specific residue.
jalemkul at vt.edu
Tue Aug 19 14:21:41 CEST 2014
On 8/19/14, 8:17 AM, Dawid das wrote:
> Right, I figured that out but in my groups when I run g_rms:
> Group 0 ( System) has 32645 elements
> Group 1 ( Protein) has 3470 elements
> Group 2 ( Protein-H) has 1772 elements
> Group 3 ( C-alpha) has 217 elements
> Group 4 ( Backbone) has 653 elements
> Group 5 ( MainChain) has 869 elements
> Group 6 ( MainChain+Cb) has 1065 elements
> Group 7 ( MainChain+H) has 1076 elements
> Group 8 ( SideChain) has 2394 elements
> Group 9 ( SideChain-H) has 903 elements
> Group 10 ( Prot-Masses) has 3461 elements
> Group 11 ( non-Protein) has 29175 elements
> Group 12 ( Water) has 29115 elements
> Group 13 ( SOL) has 29115 elements
> Group 14 ( non-Water) has 3530 elements
> Group 15 ( Ion) has 60 elements
> Group 16 ( NA) has 31 elements
> Group 17 ( CL) has 29 elements
> Group 18 ( Water_and_ions) has 29175 elements
> I don't have a group I am interested in. Should I create new index.ndx
> file? If so can I create it after the simulation, add new atoms group (CH6
> residue) and extract the information from simulation for my CH6 residue?
That's exactly how index groups work.
> 2014-08-19 13:12 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>> On 8/19/14, 8:10 AM, Dawid das wrote:
>>> Dear Gromacs experts,
>>> How can I calculate RMSD as a fucntion of time for one residue in my
>>> protein? Let's say I have a part of my sequence:
>>> ...-Phe-Ala-Ser-CH6-Tyr-Met-Cys-Gly-... . Now I want to get a plot of
>>> versus time for CH6 (my newly introduced residue).
>>> I can't find such an option in g_rms and what g_rmsf -od is not what I am
>>> interested in or I understood something incorrectly.
>> g_rms will do whatever you want if you provide the right index group.
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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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 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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