Re: [AMBER] Errors while attempting .prmtop file production

From: David A Case <>
Date: Tue, 14 Oct 2014 15:12:15 -0400

On Tue, Oct 14, 2014, Evans, Shalton wrote:
> I'm attempting to equilibrate a mixture propylene carbonate and ethylene
> carbonate at constant pressure. But, first I would have needed to create
> the .prmtop file for the system. The .mol2 file for each molecule was
> created with charges via Spartan. When I attempt creating the .frcmod
> files, I successfully make them with most of the parameters equal to
> zero and prompted with, "ATTN, need revision". I really don't know these
> values in order to replace them with their true values
> O.3 0.0000 0.0000 ATTN, need revision
> C.3 0.0000 0.0000 ATTN, need revision
> C.2 0.0000 0.0000 ATTN, need revision
> H 0.6000 0.0157 same as hn
> O.2 0.0000 0.0000 ATTN, need revision

You need to assign atom types that Amber knows about. I'd suggest taking the
mol2 files and running them through antechamber. This will use GAFF atom
types, and the parmchk program should know what initial values to assign.

You can compare the charges you get with antechamber to those you already
have, and try to make some decisions about what you like better. The R.E.D.
server is another possibility.

...good luck...dac

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Received on Tue Oct 14 2014 - 12:30:04 PDT
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