From: Mao Xiang (swallowswift_at_yahoo.com)
Date: Thu Jun 08 2006 - 22:32:06 CDT
Hello, everyone:
I am doing MD on a protein with phosphorylated
tyrosine using NAMD. I patched TP2 to that tyrosine,
and used par_all27_prot_na_qm.prm as parameter file to
run minimization (this file has parameters to the
patch atoms of TP2). I check these parameters, they
are the same as described in your paper (JACS,127
(13), 4640 -4648, 2005). But when I took a look at the
trajectory file, I noticed that oxygen atoms of O2,O3
and O4 merge(they are almost have the same
coordinates) during minimization. I am wondering if
someone met this kind of problem before. Thank you so
much for your help.
best,
mao
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