AMBER Archive (2006)

Subject: Re: AMBER: help with antechamber - creating ligand

From: David A. Case (case_at_scripps.edu)
Date: Tue Sep 05 2006 - 21:11:52 CDT

On Tue, Sep 05, 2006, sethl_at_gatech.edu wrote:
>
> I created a mol2 file for a proflavine molecule using antechamber. When I do a
> "loadmol2" antechamber crashes...
             ^^^^^^^^^^ (LEaP, I assume).

Thanks for the report; I can reproduce the problem, and I don't see anything
wrong with the mol2 file. I've added this to the Amber bug list, and we will
try to find out what is happening as soon as we can.

For now convert this to a "prep" file:

  antechamber -fi mol2 -i proflavine_charged.mol2 -fo prepc -o \
           proflavine_charged.prepc

Then use "loadAmberPrep" in LEaP. (Seems to work for me, doesn't
segfault....)

...regards...dac

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