AMBER Archive (2005)

Subject: Re: AMBER: Solvate question?

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Mon Jun 06 2005 - 10:59:06 CDT

But I try it with water (TIP3PBOX) and methanol (MEOHBOX) and I don have this
problem. With both themolecule was solvated complidly, in contrast with the
acetonitrile box ther is space between the solvent!!

On Monday 06 June 2005 7:26 am, Carlos Simmerling wrote:
> try starting with a larger box and then equilibrating the sovent while
> restraining the protein (at constant P, check the archives since people
> ask this often about water boxes).
>
> Anthony Cruz wrote:
> >Hi user:
> >I try to solvate my protein with the acetonitrile model in
> >http://pharmacy.man.ac.uk/amber/. I download ch3cn_210.pdb, prep.ch3cn
> > and frcmod.ch3cn. I load ch3cn_210.pdb (mecn=loadpdb ch3cn_210.pdb),
> > prep.ch3cn (loadAmberPrep prep.ch3cn) and frcmod.ch3cn (loadAmberParams
> > frcmod.ch3cn) in leap and the I try to solvate my protein solvateBox
> > protein mecn 8.0. When I see the results the protein was not solvated
> > completely, their is some empty spaces between the solvent. How I could
> > solvate the protein???
> >
> >Anthony
>
> -----------------------------------------------------------------------


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