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

From: Erin Kelly <>
Date: Wed, 13 Jul 2011 15:10:42 -0500

Apparently the structure looks fine in Pymol--I ran the file through
antechamber and it produced a mol2 file in about 1 second but produced no or sqm.out, is this correct? I've attached the mol2.


On Wed, Jul 13, 2011 at 2:59 PM, Erin Kelly <> wrote:

> 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.
> Erin
> 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 - 13:30:03 PDT
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