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 :( James
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