AMBER Archive (2009)

Subject: Re: [AMBER] Am I doing the right thing

From: nicholus bhattacharjee (
Date: Tue Jul 28 2009 - 23:36:31 CDT

Dear Bill & Ashish,
                                Thank you for replying.
                               First of all I will answer Bill. Actually I
am simulating my protein by solvating it in meoh, chcl3 and meoh. The
simulation takes less than half the time when I am solvating with chcl3 in
comparision to the other two.
                   Ashish I don't understand what do you mean by confident
enough. I have seen the PDB files generated from .inpcrd file and they do
contain meoh/chcl3/nma solvents in them. Even I have checked it by viewing
them in pymol. I know solvating in solvateoct is better option than
solvatebox. I just wanted to know that is the procedure of choosing the
solvent (by loading frcmod of the solvent) is the correct way (this is
written in the amber manual). You didn't give the detailed procedure of
using 8M urea-water mixture as solvent. I am unable to do the same procedure
like the other three for this solvent.

Thank you
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