AMBER Archive (2007)

Subject: Re: AMBER: Xleap and Hydrogens

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Nov 27 2007 - 09:08:29 CST

I am not sure if I understood it correct. Do you just want to create a
.pdb file for visualization purposes or to create inpcrd/prmtop files
which does not have any hydrogens but polar ones? If you want to create
inpcrd/prmtop for doing MD simulations, you have to have all the hydrogens
present. If you just want to remove the hydrogens, you can write an awk
script or perl script to do that. awk will be easier than perl for this
purpose.

Best,

On Tue, 27 Nov 2007, Shozeb Haider wrote:

> Hi
>
> I am trying to simulate a big protein (1408 residues). When ever I try
> to load it using XLEAP, it sticks hydrogens to it. The system becomes
> really huge. I was wondering if it was possible for XLEAP to add only
> polar hydrogens or add no hydrogens at all. I have had a look at the
> mailing lists and amber users have suggested to load the pdb file in
> XLEAP, write out a pdb file, strip the hydorgen etc etc. This doesnt
> work and XLEAP sticks the hydrogens back on the protein. And my other
> question is ...is there a way that XLEAP can remove multiple hydrogens
> from a protein without going through the pains of selecting every one
> and deleting them by hand.
>
> Any suggestions shall be much appreciated.
>
> Shozeb Haider
> University of London
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Chemistry      -                              =
  = University of Rochester      -                              =
  = Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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