AMBER Archive (2006)

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

From: Priti Hansia (
Date: Fri Jan 13 2006 - 04:51:13 CST

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?


> 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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