[gmx-users] Parametrisation of the heteroatomic pdb

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 28 13:48:58 CEST 2011

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.




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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