Thank you for your advise.
On Monday 06 June 2005 12:13 pm, Carlos Simmerling wrote:
> those have space too, just smaller. more complicated solvents
> sometimes use larger space to avoid solvent molecule overlap,
> I am not sure how that box was built but equilibrating it
> should get rid of the problem.
>
> Anthony Cruz wrote:
> >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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Received on Tue Jun 07 2005 - 13:53:01 PDT
