[gmx-users] Parametrisation of the heteroatomic pdb

[Justin A. Lemkul]

James Starlight wrote:
> Dear Gromacs users!
> 
> I've forced with some problem of preparing topology of my input pdb via 
> pdb2gmx.
> 
> My input structure( gramicidin ion chanell) consist of some heteroatoms 
> due to the presence of the non standart aminoacids in sequence: FOR, 
> DLE, DVA, ETA ( this the R isomers instad of L analogs)
> 
> 
> I've tried to parametriesed that structure via different force fields 
> but in all cases there are not suitable topologies for that aminoacids
> 
> e.g
> Fatal error:
> Residue 'FOR' not found in residue topology database
> 
> How I can solve that problem? I've tried to look for the suitable itp 
> file but could not find it too :(

For new protein residues, you do not need an .itp file, you need a suitable .rtp 
entry such that pdb2gmx can incorporate it into your topology.

http://www.gromacs.org/Documentation/How-tos/Parameterization
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin

-- 
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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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