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

From: David A Case <>
Date: Tue, 12 Jul 2011 16:00:47 -0400

On Tue, Jul 12, 2011, Erin Kelly wrote:
> 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?

Looks mostly good: the hydrogen attached to the C8 position of the ring is out
of the plane, but geometry optimization will probably fix that fine.

You will save yourself headaches if you use a text editor to give each
atom a unique name. If you don't really care, just add a number to each
element name, e.g. the first six atoms would become C1 though C6, etc.
I'd also take this opportunity to change the UNK to whatever residue name you
want (the one that will be in the protein pdb file you finally load in LEaP.)

> Also, if the phosphates are deprotonated, how will sqm treat
> the charge and extra electrons?

Use the -nc flag.

> 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)

Amber-type force fields don't have any concept of "bond order", so a bond is a
bond. (Actually, antechamber will assign bond orders, but they aren't really

You need to know enough chemistry to be able to look at a molecule and
determine its net charge. In your case, you have two phosphodiesters (-1
each) and a terminal phosphate (-2), so the total charge should be -4 (unless
I missed something.)

Be prepared to get a cup of coffee when you run sqm with make take a
while (less than an hour though) to get a good geometry.

...good luck...dac

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Received on Tue Jul 12 2011 - 13:30:02 PDT
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