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

From: Erin Kelly <>
Date: Tue, 12 Jul 2011 15:22:50 -0500

Ok, so we edited the PDB to add unique atom names and changed the UNK.

We used a -nc of -4, and the following error appeared in sqm.out.

QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = NaN DeltaE = NaN DeltaP = 0.0000E+00
QMMM: Smallest DeltaE = 0.1798+309 DeltaP = 0.1798+309 Step = 0

And the same error came out when editing the using the -ek flag to

qm_theory='AM1', grms_tol=0.0002, tight_p_conv=0, scfconv=1.d-8

Any suggestions?



On Tue, Jul 12, 2011 at 3:00 PM, David A Case <>wrote:

> 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
> used.)
> 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 - 13:30:04 PDT
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