Hi Prof Case,
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. Do you have any advice in this case? 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)
===========================================
Does this indicate something strange? From looking at the prmtop file, I can see the residue names WAT...but I'm not sure why it is not printing these out.
Thanx,
Maura
________________________________________
From: David Case [dacase.rci.rutgers.edu]
Sent: 03 August 2011 03:43
To: AMBER Mailing List
Subject: Re: [AMBER] Distorted waters in restrained mini
On Aug 2, 2011, at 6:11 PM, Maura Catherine Mooney <mmooney05.qub.ac.uk> wrote:
>
> Thanx for the speedy reply. When modeling cryst waters, is it best to use the triangular water model, where the two H's are bonded together?
Yes, it is best to treat all waters the same, as rigid, three-bond objects. All of the coomon water models (TIPx) require this. This isnwhybI asked how you had made your prmtop file.
...dac
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Received on Wed Aug 03 2011 - 13:00:03 PDT
