Hi Prof Case,
In the case of treating the 4 crystal waters with the TIPx model and although the waters are not part of the xleap solvation, if I simply add a bond between the two hydrogens of the waters, is this sufficient to ensure that these 4 waters are modelled with the TIPx model.
Thanx,
Maura
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: 04 August 2011 13:11
To: AMBER Mailing List
Subject: Re: [AMBER] Distorted waters in restrained mini
On Wed, Aug 03, 2011, Maura Catherine Mooney wrote:
>
> The prmtop was constructed in xleap from a stripped pdb file. I created
> a lib file using RESP charges generated with amber then neutralized and
> solvated. The four crystal waters, I think, are important for metal
> coordination and I wanted to eventually treat this region with qm (along
> with a ligand). Therefore I thought it best to model these 4 waters
> with the 'normal' geometry, as opposed to the three-bond model.
This is wrong: no matter what you eventually intend to do with QM, in the MM
force field, if you are using TIPx waters, you need to make sure that the
waters are rigid.
> Also I attempted the rdparm command on my
> prmtop and I thought the output was strange...see below:
>
> ==========================================
> RDPARM MENU: angles :WAT
> Mask [:WAT] represents 28557 atoms
>
> Angle Kthet degrees atom names (numbers)
>
> ===========================================
This looks correct: LEaP removes all the H-O-H angle force field terms in
WAT residues, unless you issue the command "set default flexibleWater on".
...good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Aug 07 2011 - 16:00:04 PDT
