AMBER: Xleap and Hydrogens

From: Shozeb Haider <>
Date: Tue, 27 Nov 2007 14:38:56 +0000

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 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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Received on Wed Nov 28 2007 - 06:07:34 PST
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