AMBER Archive (2006)

Subject: Re: AMBER: question about building molecules

From: Rita Cassia (Rita.Cassia_at_gmx.de)
Date: Mon Oct 09 2006 - 10:49:10 CDT

Thanks David!

I had solved the problem and I would like to ask someone from the list if there was already an attempt to solvate a structure in ethanol. The programm doesn't not offer a model for ethanol (I've seen that there's methanol).

Thanks in advance.

Rita

 
-------- Original-Nachricht --------
Datum: Sun, 8 Oct 2006 09:31:27 -0700
Von: "David A. Case" <case_at_scripps.edu>
An: amber_at_scripps.edu
Betreff: Re: AMBER: question about building molecules

> On Sun, Oct 08, 2006, Rita Cassia wrote:
> >
> > I had taken a look with VMD how those structures look like and I had
> seen
> > that 2 Pheophorbides were crossing each other.
> >
> > Unfortunately, when I used NAMD to start my simulation with 0° K, NAMD
> > stopped the simulation, saying that a certain atom was moving too fast
> and
> > as consequence other atoms too...
>
> You could try a minimization first, rather than MD. That might help fix
> up
> a bad initial structure. However, if the "crossing" is quite bad, this
> might
> not help either.
>
> ....good luck...dac
>
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