AMBER Archive (2005)

Subject: Re: AMBER: Antechamber/formatting question

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Fri Feb 25 2005 - 20:02:40 CST

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?

Kara

On Feb 25, 2005, at 5:31 PM, Ilyas Yildirim wrote:

>>> 3. Use your RESP charge (which came from in a different source).
>>> Since
>>> antechamber provides bcc charge that is a kind of Mulliken charge.
>>> For
>>> amber purpose, you'd better use RESP charge. In my case, I ran
>>> gaussian for my adduct. (I put a methyl group instead of including
>>> sugar and phosphate groups in this case). And applied RESP method,
>>> then modify those values into antechamber generated charges. Remember
>>> that sugar and phosphate groups' charges are constant (same as amber
>>> paper values).
>>
>> The main problem I have is generating charges. I can't generate
>> charges on a partial compound (a residue). Can you do this with RESP?
>> I don't know how to adjust the charges once the extra atoms are
>> deleted
>> and the residue created. How do you handle this fact?
>
> Kara,
>
> What kind of a residue do you have (which does not have the RESP
> charges)?
> If it is a similar residue used in AMBER, you can call the charge info
> for
> that perticular residue (which I am sure you know how to do that). If
> there is no RESP charge info in AMBER for your particular residue, you
> need to calculate it by yourself, which means u need to use an ab
> initio
> program (like Gaussian or GAMESS). Hope this helps.
>
> Good luck.
>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> - Department of Chemisty - -
> - University of Rochester - -
> - Hutchison Hall, # B10 - -
> - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> - http://www.pas.rochester.edu/~yildirim/ -
> ---------------------------------------------------------------
>
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