Hi David,
Thanks a lot for replying. I am sorry it was unclear in my problem description, but I did run antechamber on the molecules separately. I followed the following procedure: I optimized the structures in Gaussian, ran antechamber on the files separately to obtain prepi and mol2 files, then used PACKMOL to combine all the molecules together, and used LEAP to generate a topology file. So I am combining the separate molecules at the leap stage. Antechamber does give me separate atom types for graphene and PFC, but LEAP combines "c" from PFC with "ca" from the graphene. Another interesting thing is that in the topology file, the "%FLAG AMBER_ATOM_TYPE" does recognize 10 different atom types (it has separate entries for "ca" and "c"), but the "%FLAG ATOM_TYPE_INDEX" recognizes just 9. So I am assuming AMBER just uses the "%FLAG ATOM_TYPE_INDEX" to count atom types.
Thanks for the suggestion regarding water. I did not mention it in my initial email because I thought it wasn't relevant, but I am using a standard water model (SPC/Fw) for the calculations. I will look into the parameters of graphene in literature (i know people generally use a modified Tersoff potential to describe it).
Thanks,
Govind Hegde
Postdoctoral Research Associate
Chemical & Biological Engineering Department
Colorado School of Mines
________________________________________
From: David A Case [david.case.rutgers.edu]
Sent: Wednesday, June 21, 2017 6:27 AM
To: AMBER Mailing List
Subject: Re: [AMBER] LEAP Merging Atom Types
On Tue, Jun 20, 2017, Govind Hegde wrote:
>
> I am trying to set up a system in LEAP containing 3 molecule types:
> small graphene sheets, a perfluorocarbon and water. I am currently using
> GAFF, and my graphene sheets have two atom types ( ca and ha) and the
> PFC's have 6 atom types (oh, ho, o, c, c3 and f). However, when I use
> LEAP to set up my topology file, I see that LEAP ignores the "c" in the
> PFC and merges that atom type with the "ca" in graphene...
You should run antechamber on the graphene, the perfluorocarbon and water (if
needed) as separate jobs. I can't tell what really happened from your brief
description, but antechamber only handles a single molecule at a time. You
combine separate molecules into a complete system at the leap stage.
...hope this helps....dac
p.s.: I recommend using one of the standard water files: GAFF is for getting
approximate force fields for molecules where you cannot (or do not wish to)
spend time on individual optimization. If you have optimized parameters (such
as for water) you should use them. Same comment applies to graphene: there
are probably already parameters out there that people have tested.
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Received on Wed Jun 21 2017 - 09:00:02 PDT
