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
>
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Jun 06 2005 - 12:53:01 PDT
