Dear All,
I am working on amino acid mutations and I found an interesting opportunity to mutate Arginine to Homoarginine for my study. I made mutres.mtp and mutres.rtp for this mutation (R2Z) , based on the available data. I performed pdb2gmx step, after mutate.py and I got the following error.
Analyzing the answers from other forums eg and dihedrals from ffbonded.itp, I tried several ways of growing and annihilating, naming the residues. Still ended in vain. Kindly help me to overcome this error.
Did you insert the R2Z entry into the mutres.rtp and mutres.mtp files in the mutation force fields? Or are you just using these files as they are? If it is the latter, could you add the [ bondedtypes ] section to .rtp (see for example mutres.rtp in other mutation ff)
Thank you so much for identifying my mistake, Sir. I made separate files (mtp and rtp), as I was trying new mutations and not to mess with the existing ones. The rest of the processes are proper as of now.
