Re: [AMBER] Question Regarding Input File Preparation

From: David A Case <>
Date: Fri, 4 Dec 2015 08:10:24 -0500

On Fri, Dec 04, 2015, Ziheng Wang wrote:
> I am trying to generate prmtop and inpcrd files for a protein currently
> in mol2 format. I have tried to load the mol2 directly into tleap,
> change the naming to GAFF and load into tleap, convert to PDB and load
> into tleap, all without success. Can somebody recommend an approach?

General advice about asking for help:

What we need to know in order to help: *exactly* what you did (i.e. the
commands you used). You are telling us what you intended to do (e.g. "change
the naming to GAFF") rather than what you actually did.

Second: reporting a result like "all without success" is also of no help.
Please report the exact symptom or error message.

Specific advice about your problem:

Having said that, the loadMol2 command in tleap is primarily designed for
small molecules. If you have a protein, convert the mol2 to pdb (presumably
using whatever software created the mol2 file...) and load the pdb file into
tleap. For a protein, you almost certainly do not want to use the GAFF force
field; use leaprc.ff14SB, unless you are experienced enough to know for sure
that you want some other option.

...good luck....dac

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Received on Fri Dec 04 2015 - 05:30:04 PST
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