AMBER Archive (2009)

Subject: Re: [AMBER] improper torsion problem

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Jun 17 2009 - 02:47:12 CDT

> I'm running amber to see the dynamic behavior of the DNA containing
> methylated cytosine.
>
> I made mol2 file for methylated cytosine by myself, and I assigned
> appropriate amber atom type.

Did you refer to the cytosine residues in the amber ff for defining
your atom types?

> I used ff99bsc0 force field and loaded frcmod.parmbsc0.
>
> I did parmchk, and added some improper torsions to frcmod file that I
> thought they were needed.

Most if not all of the impropers needed for cytosine should already
be in the ff.

> However, the improper torsions of methylated cytosine and guanine were
> destroyed after MD simulation.

Planarity may be destroyed, but the parameters do not change.

Are you sure the impropers were imposed where you want? Probably
rdparm can tell you this. You can also use saveamberprep to save
the residue definition in a prep file, then restart leap, load
the prep file and any frcmod/parm.dat, and a pdb with the residue,
and saveamberparm. Leap will report the impropers in the IMPROPER
section (all possible ones) and list the ones it actually applies
based on the params.

And I would compare your atom types to the amber ff ones.

Bill

> I hope the attached image file will help to understand my question.
>
> Also, I attach the mol2 file and frcmod file for methylated cytosine.
>
> Thank You.
>
> Youn Kyoung @ Seoul national university
>

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