Fabrizio Mancinelli wrote:
Dear users,
in computing radius of gyration of a protein in water (g_gyrate), I have
found values that are rather smaller than what found experimentally,
maybe because bound water isn't taken into account within g_gyrate
routine. Is there any way to overcome this limitation?
yes and no.
you can reorder your waters using trjorder and then redo the
calculation. the problem ofcourse is where to stop. AFAIK these
experiments are not very accurate, as the e.g. assume spherical proteins.
Thanks in advance,
Giovanni
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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