Re: [AMBER] Query regarding the workflow

From: Pengfei Li <>
Date: Wed, 16 Nov 2016 19:05:31 -0600

Hi Abhishek,

The charge and bond information about the standard amino acid residues are stored in the mol2 files under $AMBERHOME/AmberTools/src/pymsmt/lib/ directory, that why you only need to create mol2 files for other residues for processing. Hope it clarifies things.

Kind regards,

> On Nov 12, 2016, at 3:09 AM, Abhi Acharya <> wrote:
> Hi amber users,
> I am trying to use the workflow to derive parameters for an active
> site containing Cu2+ and Ca2+ ions. The Cu2+ ion is coordinated by two
> water molecules, and active site residues Asp, His etc.
> My question is that in the input file for do we need to specify
> separate mol2 files for the two water molecules and the coordinating
> residues? In the tutorial at this link:
> the input file
> does not specify any of the coordinating His residues. But still in the 3rd
> step i.e. -i -s 3, the tutorial says that mol2 files for
> HD1, HD2 and HE1 will be created. I am a bit confused.
> I request you to kindly clarify this.
> Thanks and Regards,
> Abhishek Acharya
> CFTRI, Mysore.
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Received on Wed Nov 16 2016 - 17:30:02 PST
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