AMBER Archive (2005)

Subject: Re: AMBER: Antechamber/formatting question

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Feb 25 2005 - 19:31:46 CST

> > 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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