We have a server like http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg/submit.html in order to generate ligand topology for Gromacs. Similarly, is there an server to generate GROMACS topology for DNA & RNA bound in a protein?
Abolfazl Noorjahan
The error simply means that the residue has not been defined in the OPLS-AA. look in the file aminoacid.rtp and look for the residue names to see if there is a miss spelling or not. otherwise you have to provide that residue definition by yourself using current atom types in atomtype.atp file or you have to parametrize it by yourself.
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