Re: [AMBER] problem on heating with restraints on the solute

From: Daniel Roe <>
Date: Mon, 22 Jul 2013 12:39:42 -0600


On Mon, Jul 22, 2013 at 7:47 AM, John Travers <> wrote:
> the molecule is a noncovalent anthracene-dimethylaniline dyad held together
> via guanosine-cytidine Watson-Crick base-pairing interactions (JACS, 2001, 123, 3655, attached).
> There is no pdb structure for this molecule. so, I did the following steps
> (1). I optimized the structure using gaussian (DFT) and created gesp file (HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=8) guess=read iop(6/41=8) iop(6/50=1)).
> (2) I used antechamber (antechamber -i xxx.gesp -fi gesp -o xxx.mol2 -fo mol2 -c resp) to create a mol2 file and parmchk (parmchk -i xxx.mol2 -f mol2 -o xxx.frcmod) to create the parameters.
> (3).I solvated the molecule with a box of TIP3PBOX waters

This is not the recommended procedure for developing parameters for
use in MD simulations. Typically a "building block" approach is used
where larger molecules are logically broken down into smaller
fragments, parameterized, then linked together (e.g. proteins are
broken down into individual amino acids and parameterized with
appropriate blocking groups, see J Am Chem Soc 1995; 117: 5179-5197
and many other related papers). You may want to check out the R.E.D.
server site for tools that can help you with this

> So, these are the procedures I was using. The two fragments of the molecule are linked by hydrogen bonds, and we are interested in the effects of h-bonds on the electron transfer.

There is no concept of electrons in classical MD, so if you're
interested in electronic properties you will need to use QM.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Jul 22 2013 - 12:00:03 PDT
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