[gmx-users] atom types not found
nedomacho at gmail.com
Thu Sep 27 22:16:38 CEST 2018
Glad x2top is working out for you. The rest of the things you're
pointing out, I hope others could comment. I haven't simulated any
proteins in a long time, but if you ever need to drop a protein on the
surface of some sort of an insane molybdenum disulfide-graphene-boron
nitride heterostructure, I could be of service. ;)
On 9/27/2018 10:44 AM, pbuscemi wrote:
> This pertains the prior correspondence to building a polymer and is the process I've been developing.
> To date I can obtain an ITP and pdb from ATB for a monomer. From there with information in those files, it is relatively easy to construct the n2t file to use in x2top. ( I’d be happy to provide an example as a 'tutorial' of sorts). X2top provides the monomer rtp for use in pdb2gmx. It has all the atom type information. Thanks for the guidance on that.
> The hangups are not associated with the rtp but of all things producing the pdb of the polymer specifically positioning along,say, the x axis but more importantly, producing the pdb of the polymer that uses the same atom labels as the original pdb of the monomer. In the PE example from gromacs there are 3 mers of 2 atoms so it is easy to manually keep track of the names, but not if you have 1000 mers. Avogadro renames the added mers.
> Since gromacs can build proteins, and I can tell gmx that the monomer is a protein ( it wants to think that it is anyway), I will try to use the same logic to build the polymer. More to come.
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