AMBER Archive (2007)

Subject: Re: AMBER: Xleap and Hydrogens

From: Marius Retegan (marius.s.retegan_at_gmail.com)
Date: Tue Nov 27 2007 - 09:43:36 CST


A method for removing hydrogens from a pdb file was suggested before
in the Amber list.
http://structbio.vanderbilt.edu/archives/amber-archive/2005/1632.php
The solution in case you have problems with the link:
awk '($3 !~ /^[123]?H/ ){print}' pdbinputfile > pdbfile_nohydrogens

On Nov 27, 2007 4:08 PM, Ilyas Yildirim <yildirim_at_pas.rochester.edu> wrote:
> 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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