[AMBER] Water sigma parameters

From: Paolo Tosco <paolo.tosco.unito.it>
Date: Thu, 26 Mar 2015 20:16:44 +0000

Dear all,

I was looking at the LJSIGMA parameters in and
$AMBERHOME/dat/rism1d/model/TP3.mdl. These parameters should reflect the
van der Waals radius of the element, and indeed the value for oxygen is
the same that I can find in $AMBERHOME/dat/leap/parm/parm99.dat for the
OW oxygen.
However, according to http://ambermd.org/Questions/vdw.html, the van der
Waals radius of OW (1.768) is taken from Aqvist and should include the
water hydrogens implicitly; indeed, the radius for HW is 0.000 in
$AMBERHOME/dat/leap/parm/parm99.dat. Instead, in
$AMBERHOME/dat/rism1d/model/TP3.mdl the hydrogen LJSIGMA is 0.694. The
same is true for $AMBERHOME/dat/rism1d/model/SPC.mdl, with small
numerical differences.
Could you please explain why is a non-zero van der Waals radius for
hydrogen used for RISM1D calculations? I couldn't find an answer in the

Thank you very much in advance, kind regards

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Received on Thu Mar 26 2015 - 13:30:03 PDT
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