Hi I had a simulation run with 4.0.7, using opls-aa for a protein in water.
I now use part of the protein coordinates output from the simulation, and use pdb2gmx as: pdb2gmx -f conf.gro -ff oplsaa -ignh pdb2gmx complains that it cannot find HISB. I checked that the topology files in 4.5.3 do not contain HISB, while those in 4.0.7 do. It does not suffice to create another copy of the HISE topology in the .rtp file and call it HISB, because a number of hydrogen atoms also have been renamed? What can be done? I want to use 4.5.3 because I would prefer to retain residue numbering Maria -- Maria G. Technical University of Denmark Copenhagen
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