AMBER Archive (2005)

Subject: Re: AMBER: Antechamber/formatting question

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Sun Feb 27 2005 - 19:13:19 CST

I have a pdb of the modified guanine. My problem is the "caps". I
have charges and everything else for the modified guanine. How do I
handle removing the "cap"? When I load the DNA and my modified residue
into xLeap, it keeps the cap atoms. If I delete them, it tells me that
there is no longer an integral charge, etc. What should I do?

Kara

On Feb 27, 2005, at 11:56 AM, Ross Walker wrote:

> 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
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
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