Hi Prof Case/Prof Simmerling,
I found out what was causing the 4 crystal waters to be treated as 'normal' bonds. Because they are part of the system I want to later study with QM, I initially ran gaussian calculations for the RESP calc in amber. The 4 waters had names such as O46, O47, O49, O49, H84, H85...etc. I looked at the solvent water which are named O and H1 and H2. So I changed the names of the these 4 cryst waters to O, H1 and H2. When I look at this in Xleap now, they appear as the triangluar water models, so it looks like they will be treated in the same manner as the solvent water. In saying this, because they are to be considered part of my QM system, I need to edit the charges on these waters to correspond with my calculated RESP charges. Is this valid to do so?
I appreciate the advice.
Maura
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: 08 August 2011 13:25
To: AMBER Mailing List
Subject: Re: [AMBER] Distorted waters in restrained mini
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 - 07:00:04 PDT
