[gmx-users] Ramachandran plot for non standar residues

[Justin A. Lemkul]

Rebeca García Fandiño wrote:
> Hello,
> I am trying to calculate the Ramachandran plot for a molecules based on 
> non-standar aminoacids, parametrized with the Gaff force field and 
> simulated with Gromacs 4.0.7. 
> When I try using g_rama -f trajectory.xtc -s topology.tpr -o rama.xvy
> I get: Found 0 phi-psi combinations.
> 
> I suppose the problem is the nomenclature of my atoms, since I don´t 
> have any CA named atoms.
> 
> Is there any way to calculate g_rama for non-standar residues defining 
> the atoms I need?
> 

I think you can just change the atom names in your topology, generate a new .tpr 
file, and run g_rama again.  I don't believe atom names are stored in the 
trajectory.

-Justin

> Thanks a lot for your help.
> 
> Best whishes,
> 
> Rebeca Garcia
> Santiago de Compostela University
> Spain
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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