AMBER Archive (2005)

Subject: Re: AMBER: Solvate question?

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Jun 06 2005 - 06:26:53 CDT

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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