On Sun, Aug 07, 2011, Maura Catherine Mooney wrote:
>
> I dont remember doing anything specific in xleap to get these 4 cryst
> waters to have 'normal' geometry. They are present in the original pdb
> file. Do you think it is strange that amber treats these this way?
I think it is strange. Just to be sure: what is the residue name for the
waters in the original pdb file? Most often it is HOH, but there might be a
clue if it is something different. It's probably also worth stating the exact
list of leap commands you used -- we have to be able to reproduce the problem
before we can fix it.
Some volunteer on the list might double check how LEaP handles waters when
the system is solvated later. Or, post a list of commands that works for you.
....dac
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Received on Mon Aug 08 2011 - 05:30:04 PDT
