AMBER Archive (2006)

Subject: Re: AMBER: parmchk error

From: David A. Case (
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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to