Re: [AMBER] Antechamber trouble with COA-acyl chain

From: Erin Kelly <>
Date: Tue, 12 Jul 2011 14:40:39 -0500

David thanks for your response,

I noticed that the structure was poor, I'm new to chemdraw and its been
giving me a few problems... I have another pdb of C6-CoA, could you take a
look at it? Also, if the phosphates are deprotonated, how will sqm treat
the charge and extra electrons?

Do we need to change the multiplicity due to the double bonds in the ring
and the charged oxygens in the phosphates? How can we estimate the molecules
charge? (For the -nc flag)

By building it in pieces do you mean building files separately for the CoA
and the acyl chain and loading those separately into the protein? I was
able to load CoA alone into the protein but I'm not sure how to go about
placing both of them in the correct positions. I'm using the Sustiva
tutorial as a starting point for this work, would loading 2 be similar to
that tutorial, or would I have to go about it in a completely different way?

Thanks again,

On Tue, Jul 12, 2011 at 1:43 PM, David A Case <>wrote:

> On Tue, Jul 12, 2011, Erin Kelly wrote:
> > Here is the most recent pdb.
> >
> > > > I've been trying to produce a mol2 file from a pdb generated using
> > > ChemDraw
> This pdb file is seriously flawed, and has so many problems I hardly know
> where to begin :-)
> 1. Atoms 30 and 32 are almost on top of one another
> 2. All the phosphates are protonated (probably not what you want for
> anything
> near physiological conditions.
> 3. Oxygen atom 10 is less than 1 Ang from a neighboring nitrogen.
> 4. The adenine ring is highly reduced and is virtually unrecognizable.
> etc.
> Even with a good starting structure, this molecule would be a challenge:
> the
> am1-bcc prescription requires a (local) minimum at the AM1 level, which
> will
> take a while to find for such a big molecule. It probably could be made
> to work (be patient) if you had a good starting structure, but you might
> want
> to consider building this molecule in pieces.
> ..dac
> .
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Received on Tue Jul 12 2011 - 13:00:03 PDT
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