Hi Carlos,
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'm little experienced in this area, and always open for discussions, advice or suggestions. Would you expect xleap to treat any residue called WAT with a TIPxP model, or could it be that because it not's part of the solvation carried out in xleap it is treated as the 'normal' water.
Maura
________________________________________
From: Carlos Simmerling [carlos.simmerling.gmail.com]
Sent: 04 August 2011 13:18
To: AMBER Mailing List
Subject: Re: [AMBER] Distorted waters in restrained mini
How did you make these have a "normal" geometry? What commands or parameters
do this?
On Aug 3, 2011 3:59 PM, "Maura Catherine Mooney" <mmooney05.qub.ac.uk>
wrote:
> 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 Sun Aug 07 2011 - 16:00:03 PDT
