Re: [AMBER] Error while running leap for a protein containing Co2+

From: Kenneth Huang <>
Date: Mon, 8 Jun 2015 10:21:23 -0400


You might want to check out one of the advanced tutorials by Pengfei on the
amber site for getting parameters for metals in proteins- I think it's 18?

Also, I feel obliged to point out that unless you have a specific reason
for sticking to AmberTools12 (which I'm assuming you're using), then you
should upgrade to Amber15, especially since I think some of the things for
this were updated in the AmberTools15 release.



On Mon, Jun 8, 2015 at 8:05 AM, Suchetana Gupta <> wrote:

> Dear AMBER Users
> I am trying to run LeaP for a metalloprotein. Cobalt 2+ is the metal
> involved. Here is the input of my file:
> source leaprc.ff99SB
> source leaprc.gaff
> loadoff atomic_ions.lib
> #i know I should add a frcmod file here with vdW parameters for Co
> ACHE = loadpdb cda_co.pdb
> savepdb ACHE cda_co_out.pdb
> saveAmberParm ACHE cda_co.crd
> quit
> The error that I am getting is
> Building topology.
> Building atom parameters.
> For atom: .R<CO 230>.A<CO 1> Could not find vdW (or other) parameters for
> type: Co2+
> Parameter file was not saved.
> Quit
> I use AMBER12.
> How do I go about solving it?
> Not able to locate vdW parameters for Co2+ anywhere. Can someone please
> share?
> Thanks
> Suchetana
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Received on Mon Jun 08 2015 - 07:30:03 PDT
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