Re: [AMBER] Fatal error atom type work around

From: David A Case <>
Date: Mon, 31 Aug 2020 15:53:01 -0400

On Mon, Aug 31, 2020, Ayesha Fatima wrote:

>I would like to share my experience on the above error. I had this error
>even when I followed the correct list of commands. My work around was like

Thanks for the feedback. Your workflow is more complex that what most
Amber developers would use. See comments below for some ideas; but
there is no one "right" way to do things. A lot of the problem seems to
come from the RED server, so maybe some of those rough edges can be
smoothed out.

>3. convert ligand file to mol2 file using DS or pymol or chimera
>4. parse ligand.mol2 file to antechamber using to get the gaff atom type.
>4b. Use the RESP charges to replace any charges that may be generated by the
>antechamber program in the ligand.mol2

>The only hassle now is the conversion of mol2 file generated by the RED
>server into mol2 file with gaff atom types.

Antechamber by default will give you gaff atom types. You might consider
first running antechamber with no charge model, then copying (by hand or
through a script) the charges from RED into the mol2 file that antechamber
creates. This sounds like what you would get from the three steps you
list above, and you don't have to do any worrying about gaff atom types.

...good luck....dac

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Received on Mon Aug 31 2020 - 13:00:04 PDT
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