AMBER Archive (2006)

Subject: Re: AMBER: problem in saving parameter file for non-standard residue

From: Ilyas Yildirim (
Date: Fri Jan 13 2006 - 05:10:52 CST

Dear Priti,

This is a very hard subject; how to find/define the missing parameters.
You may find a similar structure in literature, or in AMBER, which is
similar to your non-standart residue, and then assume that the equilibrium
bond lengths, angles, the force constants, etc., are same as the similar
structure. Other than that, the hardest way is to calculate the missing
parameters, which needs x-ray structure, MD simulations, etc. I would
suggest u to first scan the literature and see if there is any similar
structure. If yes, use those parameters in your structure. Good luck...

On Fri, 13 Jan 2006, Priti Hansia wrote:

> Dear Ilyas,
> Thanks a lot for your prompt reply. I was hoping to get some answer like
> this since my non-standard residue is connected to the pdb. Now, the
> question is to describe the missing angular and dihedral parameters. Is
> there a straightforward way of doing this in Amber?
> -priti
> > Dear Priti,
> >
> > I think the reason is very obvious; your frcmod file is missing
> > the necessary parameters to describe the .pdb file. Your frcmod file is
> > created for the .prepin file. When your non-standard residue is in a
> > structure, it is bonded to at least one residue. And when it is bonded, u
> > need to describe the missing parameters. For instance, let's
> > say that the head atom of your non-standart residue is an 'S', with an
> > atom type 'sh'. This atom will have a bond with the next residue. And
> > let's say the tail atom of the next residue is a 'C' with an atom type
> > 'C'. U need to describe, for instance, the bond length of 'sh-C'. This is
> > just the simplest case. U need to describe the missing angular and
> > dihedral parameters,etc. too.
> >
> > Hope this helps. Good luck.
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  Ilyas Yildirim
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