AMBER Archive (2003)

Subject: Re: new amino acid residues

From: David A. Case (case_at_scripps.edu)
Date: Thu Jan 30 2003 - 11:46:35 CST

On Thu, Jan 30, 2003, Nick Polfer wrote:
>
> I am trying to make some new amino acid residues which are only slightly
> different to ones existing in AMBER. I have followed the antechamber
> procedure, generated new charges using G98 and resp, have successfully got
> a name.prepin and corresponding frcmod files.
>
> Should I stick with the gaff suggested parameters or could I (my preferred
> route) 'translate' these into parm99.dat format atom types?

You could do either, but I would advise the route of using parm99 atoms types
for a modified amino acid.

>
> Since I want to use these residues to make peptides (in Xleap) which I
> then want to compare to other peptides completely generated from standard
> AMBER residues, I would prefer if they could all be in the same format.
>
> Can somebody please advise me on the flags I need to use to convert the
> format either in antechamber or xleap?
>

I think you just need to use a text editor: take the prepi file you have,
and change the atom types (and charges, if needed) to the parm99 types.
Update the frcmod file in a similar way.

Antechamber in principle can handle parm99 atom types, but is really designed
to use the gaff types. A little hand-editing is probably required here to
be sure you are getting exactly what you want.

..hope this helps....dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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