Dear all,
(I apologize if this question has been asked and answered before)
is there a canonical way in the Amber community to add ions (e.g. Na+
and Cl-) not for charge neutralization of the protein system, but to
create a given (e.g. physiological) salt concentration in the solution?
In the Amber mail archives I found a perl script from Thomas Cheatham
that computes the number of necessary molecules from a given volume.
Of course, these ions can then be added with leap.
However, when I tried it once for a single system, all ions appeared
rather crowded and were not distributed in an approximately uniform way
in the solvent box; this could have been an outcome of my system, of course.
So my question is: How do other people deal with this?
Thanks in advance for your advice.
Regards,
Anselm
Bioinformatik
Friedrich-Alexander-Universität Erlangen-Nürnberg
Germany
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Received on Tue Apr 20 2010 - 06:30:03 PDT
