Re: [AMBER] Trouble making frcmod file (ultimately to create prmtop file)

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 6 Oct 2014 16:42:53 -0400

On Oct 6, 2014, at 4:34 PM, Evans, Shalton <shalton.ccs.msstate.edu> wrote:

> Hello All,
>
> Perhaps someone can help me with this possibly trivial but annoying problem. I'm trying to simulate a half lithium battery with elements ethylene carbonate, propylene carbonate, lithium ions and graphitic sheets. I loaded all .mol2 files for my system in antechamber separately and obtained .frcmod files. But, the .frcmod files don't have but one or two values per file. Where I don't have values the prompt "ATTN, need revision" appears. A copy of it is pasted below. I read on one of the tutorials that if this happens I will need to fill in the 'zeros' and estimate these values on my own. Does anyone have the same problem while doing this as well? Is there something Im missing? A response would be really appreciated.
>
> MASS
> O.3 0.000 0.000 ATTN, need revision
> C.3 0.000 0.000 ATTN, need revision
> C.2 0.000 0.000 ATTN, need revision
> H 1.008 0.161 same as hn
> O.2 0.000 0.000 ATTN, need revision

Where did you get these atom types from? The typical workflow is to go through antechamber, which parses a structure, runs a QM calculation on it to minimize and extract charges from that molecule, then it determines atom types and the connectivity.

This atom typing is critical, since that will tell Amber what kind of atom it is and allow it to determine what parameters should be used to describe its interactions with other atoms.

The O.3, C.3, C.2 and O.2 atom types listed above donít look at all familiar to any force field Iíve seen in Amber. As a result, parmchk canít find any matches in the force field databases, so it spits out 0s with an ATTN, need revision.

The solution is better atom typing, in which case many (or all) of these problems should resolve.

HTH,
Jason

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Oct 06 2014 - 14:00:03 PDT
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