AMBER Archive (2006)

Subject: Re: AMBER: parmchk error

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 14 2006 - 22:28:20 CDT

On Mon, Jun 12, 2006, Evan Kelly wrote:
>
> As per the conversation below, here are the inputted (to
> antechamber) .pdb file and the resulting prepi file. I call parmchk as:
>
> parmchk -i VLB.prep -o VLB.frcmod -f prepi

Try the following (works for me):

antechamber -i VLB.pdb -fi pdb -o VLB.mol2 -fo mol2
parmchk -i VLB.mol2 -f mol2 -o foo

We are really encouraging everyone to use the mol2 format rather than the
prepi/prepc formats. Junmei may be able to track down and fix the bug
in parmchk with prepi input, but until that happens, I hope the above
will provide a workaround.

The "prep" formats will probably be retired in future versions of Amber,
so see if using mol2 will serve your needs.

Thanks for the report....regards.....dac

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