Re: [AMBER] RMSD and reference structure

From: Jason Swails <>
Date: Tue, 18 Jan 2011 00:13:52 -0500

On Mon, Jan 17, 2011 at 11:45 PM, Siti Mohamad <>wrote:

> Dear AMBER,
> I am calculating rmsd for my system by comparing it to reference structure
> (
> .pdb). The pdb file created using ambpdb on the restart and prmtop file.
> However, when I checked the atom names, some of them are different from
> prmtop file, eg:
> RG
> .prmtop .pdb
> atom H21 1H2
> atom H22 2H2

This can be disabled. Use the "-aatm" flag in ambpdb to disable this
behavior. The issue is that the PDB file formats have changed, and ambpdb
tries to satisfy everyone, but it has to pick a default behavior. -aatm
will use left-justified Amber atom names.

> Will this effect the ptraj to do rmsd? Or should I change the atom names in
> pdb file to be similar to prmtop file?

I don't think it'll make any difference, but like I said it's a simple
change to the ambpdb command to generate a name-compatible PDB file.

> Can I use restart file as reference structure?

I don't know. The manual is not very helpful on this point. All I can
suggest is try it and see if you get the same answer either way.

Good luck!

> Thanks.
> Regards,
> Siti
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Jan 17 2011 - 21:30:08 PST
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