[gmx-users] atom types not found

[paul buscemi]

Alex,

There are so many important  reactions / applications in which protein polymer interactions play a role that  the ability  to generate  of polymers should be part of gromacs repertoire. I’ll keep plugging away on this and report to the community if I can break the code  - other than using the very good but terribly expensive commercial programs.   I would not doubt that many have already accomplished this this task, but it is not well tracked within this group.

I might not approach a Molysulfidnitride substrate , ( making turbine blades ??)  but TiO2 is indeed another surface very popular with proteins.  Most every nitinol surface is essentially TiO2.  If you have some pointers on that,  I’m listening.

Thank you again for the assist.

Regards
Paul

> On Sep 27, 2018, at 3:16 PM, Alex <nedomacho at gmail.com> wrote:
> 
> Hi Paul,
> 
> 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. ;)
> 
> Alex
> 
> 
> On 9/27/2018 10:44 AM, pbuscemi wrote:
>> Alex,
>> 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.
>> 
>> Paul
>> 
>> 
>> 
> 
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