From: Eifler, Jay Q. (UMKC-Student) (jqewt2_at_mail.umkc.edu)
Date: Mon Jul 14 2014 - 13:05:36 CDT
I cannot find a reference on how NAMD adds its hydrogens.
Chimera fully explains for example.
I also am wondering if I use another program to add hydrogens
but then minimize my structure in NAMD doesn't that
just readjust the hydrogens to NAMD's force field parameters?
So then shouldn't we just use NAMD's add hydrogens facility
rather than other methods to be consistent? I've noticed that
neutral protonations just adjust back to the odd looking structure
with a hydrogen apparently deleted.
Maybe I have some confusion about the hydrogens. Also,
I thought they were held rigid with SHAKE or something.
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