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

From: Erin Kelly <>
Date: Wed, 13 Jul 2011 14:59:03 -0500

Hello again,

I've editted the original pdb with the coordinates from Dr. Case (thank you
for this information!), there seems to be a problem with one of the
phosphate groups (technically phosphite PO3)--when I look at it in VMD the
group is separate from the rest of the molecule. I don't know why it isn't
connecting to the oxygen (P3-O9). Is this effect simply because the
phosphate is further from the oxygen than that particular bond length would
be so VMD doesn't recognize them as connected? Also, wouldn't this have had
a major effect on the final optimized conformation from the (ie
different electron density around free phosphate vs one bonded to O)?

I've attached the modified pdb.

Any insight would be greatly appreciated.


2011/7/13 David A Case <>

> On Wed, Jul 13, 2011, Erin Kelly wrote:
> >
> [posted a pdb file for coA]
> OK: I've looked at this, and sqm indeed has trouble with this structure.
> We've seen this before for some other structures: systems with a bad, but
> not
> impossible, starting geometry, sometimes won't converge with sqm. I
> haven't
> tried tweaking the convergence parameters that are available, however.
> On the other hand, good old Gaussian seems to have no trouble with this,
> and
> optimizes the geometry. If one then takes that geometry and feeds it to
> sqm,
> sqm has no problems. So: sqm needs some work on convergence. However,
> antehcamber also (for other reasons) needs pretty good starting geometries
> --
> it's just hard to say what "pretty good" means in this context.
> I'm attaching two sqm input files:, derived from the so-so geometry
> that Erin came up with; and, which uses the Gaussian-optimized
> geometries.
> Erin can paste the "g09" coordinates back in to a pdb file, and should be
> able
> to get antechamber going from those.
> Amber-developers might want to see if they can find out how to fix the
> problem
> with the "" file.
> ...regards...dac
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Received on Wed Jul 13 2011 - 13:00:04 PDT
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