AMBER Archive (2004)

Subject: Re: AMBER: sander.QMMM: CHARGE keyword in file

From: M. L. Dodson (
Date: Wed Aug 04 2004 - 19:08:07 CDT

On Wednesday 04 August 2004 03:48 pm, Ross Walker wrote:
> Dear Bud,
> > A question about sander.QMMM (AMBER8) input.
> First question, have you applied bugfix.13? If not, do this first of all
> before you do ANY QMMM calcs.

Hi Ross,

I _think_ I did (I applied bugfix.all, IIRC), but I will check
explicitly tonight.

> The charge you specify in should be just the charge on the QM
> system. Bare in mind however that any bond you break will have hydrogen
> atoms added in the QM region. E.g:
> H H H H QM region = C1 and C2 H H
> HC1-C2-C3-C4H ------------------------> HC1-C2H Charge =0
> H H H H H H
> Hence check if you are breaking bonds and where. Then for every bond you
> break add a hydrogen on the QM section and at the end of it see what you
> are left with. Then calculate charge of this QM piece and set that in the
> file.

Hmmm... That was my interpretation (in analogy with the full
DivCon version, MOPAC, etc). I'll email you my input files Fri
(I'm out tomorrow, and it is 6:50PM here at home). Briefly,
though, the QM section of the run that failed is a dinucleotide + a
carboxylate + a protonated amine, total charge of -1 (including
the internucleoside phosphate):

5'O-nside1-3'O-PO_2-5'O-nside2-3'O (flanked by the rest of the DNA
treated via MM). Plus the carboxylate and amine (residues on the
enzyme). Two link hydrogens cap the 5'- and 3-hydroxyl oxygens
(plus several for residues on the enzyme). CHARGE=-1 => "odd
number of electrons in closed shell calculation" (or some such).

The system that ran to completion with no error message left out
the central PO_2, so would have two more link hydrogens in place
of the phosphorus and two oxygens. CHARGE=0 => runs OK, but
3'-sugar ring opens between C3' and C4'. Oops!

So it could be the bugfix problem, unless I've missed something.

Thanks! I'll send the files via private email on Fri.


> If you still have problems please email me your input files and I'll take
> a look and see if I can get it to run.
> All the best
> Ross
> /\
> \/
> |\oss Walker
> |
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- |
> | | PGP Key available on request |

M. L. Dodson                      
409-772-2178                                FAX: 409-772-1790

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