Re: [AMBER] Stripping hydrogens etc. from the prmtop?

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 8 Feb 2012 00:17:54 -0500

There will be a program in the upcoming amber release that is capable of doing this (ParmEd), but nothing that is out right now.

It would be difficult to get leap to do this since you would have to define all new residues that did not have the hydrogens present and load that library instead of the default.

Note that leap doesn't just add hydrogen-- it adds any atom that's in the library template that is not in the pdb.

On to other comments -- doing this will almost certainly result in a topology file that is worthless for standard MD. If you're using it for visualization or something like that you're ok, but you would have to be running some strange calculations with a novel method to actually make use of such a topology file in simulation.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Feb 7, 2012, at 3:43 PM, "Cihan Aydin" <cihan.aydin.umassmed.edu> wrote:
> Hi all,
> 
> Is there a way to...
> 
> 1- Strip hydrogens or any other atoms that I want from the prmtop (not 
> only waters)?
> 2- Create topologies using any version of leap without adding hydrogens 
> or other atoms?
> 
> or do any of you have some kind of third party software or code 
> modification to achieve that?
> 
> Thanks,
> 
> Cihan
> 
> -- 
> Cihan Aydin
> 
> University of Massachusetts Medical School
> Department of Biochemistry and Molecular Pharmacology
> PhD Candidate, Schiffer Lab
> 
> 364 Plantation St LRB 970M
> Worcester, MA 01605
> 
> cihan.aydin.umassmed.edu
> 
> 
> 
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Received on Tue Feb 07 2012 - 21:30:03 PST