Re: [AMBER] Off , mol2 and frcmod files

From: David A Case <>
Date: Tue, 9 Aug 2016 09:56:40 -0400

On Tue, Aug 09, 2016, Christopher Jesudason wrote:

> If I have an off (library) file and a pdb file for molecule A (say
> A.lib abd A.pdb respectively) , I noticed that antechamber and parmchk
> does not read off file format inputs, inputs are -f format (prepi,
> prepc, ac ,mol2) : outputs are a different matter. If I wish to
> produce an frcmod file for molecule A (residue A) A.frcmod in
> conjunction with A.lib , is there a direct method to produce the
> frcmod file relative to the off file which is needed to fully specify
> all the parameters for a molecular dynamics run by then loading these
> files in tleap to produce the prmtop and input coordinate files ?

This should work (untested):

in tleap, use loadOff and saveMol2 to convert the lib file to mol2.

then use the resulting mol2 file in the usual way as input to parmchk2 to
create a frcmod file.

...hope this helps...dac

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Received on Tue Aug 09 2016 - 07:00:03 PDT
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