[gmx-users] Parametrisation of the heteroatomic pdb

James Starlight jmsstarlight at gmail.com
Fri Oct 28 11:37:57 CEST 2011

Dear Gromacs users!

I've forced with some problem of preparing topology of my input pdb via

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

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 :(

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