RE: AMBER: Antechamber/formatting question

From: Ross Walker <>
Date: Sun, 27 Feb 2005 11:56:18 -0800

Dear Kara,

> I need to covalently bond a minor-groove binding agent to a 10-mer
> strand of DNA by attaching it to a guanine. I guess I could get the
> charges for the guanine portion (in a DNA strand) and I can get
> antechamber to give me the charges for the drug, but It's
> attaching the
> drug to the guanine (atoms must be deleted and then the charges
> adjusted so the overall charge of the new residue is correct.
> This is
> where I'm having problems. Any hints?

Why not create yourself a brand new residue that is essentially a modified
Guanine. I.e treat the guanine and bonded drug molecule as a single residue.
You can then resp fit this whole molecule (with approiate caps around the
Guanine). You can do all this with xleap by creating a pdb containing a
standard Guanine and the drug molecule and calling them the same residue
name e.g. GXX. Then load this pdb into xleap, it will complain about unknown
atoms etc. Go to the editor, draw in bonds where you want them, delete atoms
you don't need etc. Then save this as an off file in leap and also as a pdb
file. Then use the pdb file for you resp fitting,fire up xleap again, open
the off file edit the molecule and the charges, atom types based on the
default guanine template and the GAFF atom types assigned by antechamber for
your drug molecule, etc. Create an frcmod file with any of the missing
parameters and then you can use this off file and frcmod file as templates
for when you load your main structure pdb (assuming you have moved the drug
and guanine next to each other in the pdb and called them resiude name GXX).

In this way you won't need to do any fudging with respect to resp. You will
also hae a library file of this residue combination for use in other
simulations that share this configuration.

I hope this helps.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Sun Feb 27 2005 - 20:53:00 PST
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