I created a library file for amber in order to then create the prmtop and inpcrd. This *.lib included the generated RESP charges (for the QM system) and some atom type changes. For creation of the prmtop/inprcd, I load this lib into xleap then neutralize and solvate and then save the prmtop and inprcd. My protocol is solute restrained mini1, unrestrained mini2, classical (md1) heating, classical (md2) equilibration, then switch to qmmm (md2) equilibration and qmmm (md3) production. Is is best to run mini1 mini2 cmd1 and cmd2 then create a new prmtop with the edited charges for qmd2 and qmd3. I'm not sure what is the best way to proceed, if I want to include my calculated RESP charges for this system.
Thanx,
Maura
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: 08 August 2011 15:12
To: AMBER Mailing List
Subject: Re: [AMBER] Distorted waters in restrained mini
On Mon, Aug 08, 2011, Maura Catherine Mooney wrote:
>
> 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?
No, you should not need to edit the charges. Once you run the QM part,
whatever charges were in the MM section will be ignored. *Before* you get
to the QM calculations (e.g. for equilibration) you most likely want to
use a standard water model.
...good luck...dac
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Received on Mon Aug 08 2011 - 07:30:03 PDT
