Re: (2) Re: AMBER: F,Cl,Br,I in MMPBSA

From: David A. Case <>
Date: Fri, 21 Oct 2005 08:31:06 -0700

On Fri, Oct 21, 2005, Yong Xu wrote:
> I use following procedure to prepare lig.frcmod and lig.prep file and encounter some problems
> ===============================================
> give a ligand's MOL2 file, lig.mol2
> antechamber -i lig.mol2 -fi mol2 -o lig.gjf -fo gcrt
> g98 <lig.gjf> lig.out
> antechamber -i lig.out -fi gout -o lig.prep -fo prepi -c resp

Use "-fo prepc" or "-fo mol2". The latter is better, since we are recommending
that in general people use the mol2 format rather than prep (which will
eventually be phased out.)

It looks like there is a bug in the prepi code. The author, Junmei Wang reads
this reflector, so maybe he will be able to track it down.


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Received on Fri Oct 21 2005 - 16:53:00 PDT
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