how can i renumber .gro and .top residue numbers to start with a specific number. The scenario is that i have first 40 residues of DNA and i dont want to disturb them. I just want to renumber from where my aminoacid residues start. so in short i just want to renumber my aminoacid residues only nothing else. Help will be very much appreciated
Hi,
You could use, gmx genconf -renum to renumber your gro file. Coming to topology. I think if the pdb file has "TER" at the end of each section, DNA and Protein respectively, the pdb2gmx must have made separate topology files. I have never worked with DNA, so I am not so sure. I am sure you must have chosen a forcefield that supports both DNA and protein for your simulation. Otherwise, It's better to get DNA topology using QM (gaussian) or any other supported browser and incorporating the same as .itp file (basically treating DNA as a ligand).
Hope it helps.
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