AMBER Archive (2006)

Subject: RE: AMBER: parmchk error

From: Junmei Wang (
Date: Thu Jun 15 2006 - 10:16:10 CDT

With the latest version of antechamber package, I can run parmchk
properly for the prep input. But Dave's suggestion is very good: one
should try to use mol2 or ac (both have the atomic connectivity table)
instead of prep. For a molecular format that has no atomic connectivity
table, such as prep, it is possible that the program makes a wrong
judgment on bond formation if the molecular structure is not good


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
> 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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