Re: AMBER: Mol2 to prepin file conversion

From: David A. Case <>
Date: Thu, 26 May 2005 17:44:36 -0700

On Fri, May 27, 2005, Andrew Box wrote:

> I have been trying to intercalate a drug into a 6 base pair sequence of DNA
> and covalently attach the drug.
> The molecule contains 463 atoms.

Antechamber wants to work with bite-site pieces, not with the entire drug+DNA
complex. Here is what you need to do, roughly:

1. extract the drug by itself, and add hydrogens (or methyls or whatever) to
    make this into a legitimate closed shell molecule.

2. Run this through antechamber to get charges and force field parameters;
    bcc charges should be fine for a first go-round.

3. manually remove the capping groups, and read in the DNA and the drug mol2
    file you just created. You may have to tweak the charges near the joining
    point so that the overall charge is what you want, but this is generally
    not that hard. Use LEaP to add the covalent bond between the drug and the

This should get you a working structure, with "pretty reasonable" (tm)
charges. There are more elaborate and systematic ways to develop the charges,
which others reading this reflector may point you to. But the procedure
given above is still a good starting point, since the more elaborate methods
will just alter the charge distribution. So, my suggestion is to try this
approach, make sure that things seem stable, etc. first.

....good luck...dac

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Received on Fri May 27 2005 - 01:53:01 PDT
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