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 Thu Aug 04 2011 - 05:30:04 PDT
