AMBER Archive (2006)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jan 13 2006 - 10:44:12 CST

Dear Priti,

If you used antechamber to build your non-standard residue then it will have
defined the atom types and any missing parameters based on the gaff force
field. This force field can be used in addition to the regular FFXX force
fields since it uses lower case atom types. In this case your parameters
have not been found because you did not load the gaff.dat file into leap.

Start Leap as you have been doing and then before you load your non standard
residue and pdb etc type:

loadamberparams gaff.dat

You should then be able to load your non-standard residue and pdb and then
save the prmtop file.

Note, you may also need to load the frcmod file antechamber created if
necessary. You should also look at the atom types and parameters antechamber
assigned with reference to the GAFF force field paper and make sure they are
what you would expect...

Note: you should probably work through the following tutorial:

http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_five/index.htm

This will give you a better understanding of what Antechamber is doing.

All the best
Ross

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|\oss Walker

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Priti Hansia
> Sent: Friday, January 13, 2006 02:51
> To: amber_at_scripps.edu
> Subject: Re: AMBER: problem in saving parameter file for
> non-standard residue
>
>
> 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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