AMBER Archive (2009)

Subject: Re: AMBER: CHCl3 solvent box

From: WJ Ding (strollingforever_at_gmail.com)
Date: Mon Jan 05 2009 - 15:21:32 CST

Yes. I used the CHCL3BOX unit to build my slvent box. Is there any other
way to do this?

About C-Cl cleavage which I worried about,I remember I have eve run a MD
calculation and found the C-Cl bond to be cleaved. But I will do a test
claculation to make sure about this. Thank you so much.

Have a good day.

WJ

2009/1/5 David A. Case <case_at_biomaps.rutgers.edu>

> On Mon, Jan 05, 2009, WJ Ding wrote:
>
> > I built a solvent box of chloroform with tleap. When I visualized the pdb
> file
> > with VMD, it is found that the bond lengths of C-Cl even in the same
> molecule
> > are different (1.72-1.83 angstrom, I just cheked three molecules), which
> will
> > cause the C-Cl bond to be cleaved during the MD calculation. I do not
> think tt
> > is reasonable. Is there anyone who ever encountered this problem?
> What's
> > wrong with my solvent box?
>
> Bonds can never be cleaved in MD simulations -- why not minimize or run
> dynamics and see what happens.
>
> You didn't say how to created the solvent box, but my guess is that you
> used the CHCL3BOX unit. This file indeed has unequal C-Cl bond lengths
> -- it could be a snapshot from an MD simulation, although the magnitude
> of the deviations from ideality seems large.
>
> ...dac
>
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