thought of that, but the trajectory also has HISB data .. so I guess I will have to alter it frame by frame ?
On Thu, Jun 16, 2011 at 4:32 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 16/06/2011 11:01 PM, maria goranovic wrote: > >> 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 >> > > Rename all the HISB residues in your input coordinate file to whatever > OPLS/AA wants. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Maria G. Technical University of Denmark Copenhagen
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