Hi Prof Case,
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? I see that this is used in solvation in AMBER. However, why should these waters not be treated in a similar manner (prmtop built with ff99SB), without actually building the H-H bond? Additionally, if there is a discrepency in the prmtop angles, what would be the best method to resolve this?
Many Thanx,
Maura
________________________________________
From: David Case [dacase.rci.rutgers.edu]
Sent: 02 August 2011 22:57
To: AMBER Mailing List
Subject: Re: [AMBER] Distorted waters in restrained mini
On Aug 2, 2011, at 5:48 PM, Maura Catherine Mooney <mmooney05.qub.ac.uk> wrote:
>
> I have a problem with a simulation i'm running. I have a pdb file, which I have stripped and contains only protein, ligand, divalent metal and 4 cryst. waters (I removed the CONECT records etc). When I run a standard restrained minimization (similar to the restrained minimization protocol in Ross's tutorials) the 4 cryst. water appear distorted and only have a HOH angle of ~18degrees. Upon running a 2nd minimization, unrestrained the problem still persists and again the same, after a solvated cmd1 heating. The stripped pdb file looks fine, however, so I'm not sure what's going on. Has this been previously encountered? Could it be an imaging problem or is there some deeper problem?
>
How did you prepare the prmtop file? It sounds like the crystal waters might not have the H-H "bond" that keeps solvent waters rigid. You can use rdparm to print out all the bonds and angles in your prmtop file, and see if there is something different between crystal waters and the others.
....dac
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Received on Tue Aug 02 2011 - 15:30:03 PDT
