AMBER Archive (2008)

Subject: Re: AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water

From: David A. Case (case_at_scripps.edu)
Date: Mon Apr 07 2008 - 15:40:27 CDT

On Mon, Mar 31, 2008, Markus Kaukonen wrote:
>
> I tried to reproduce article data Simonson et al
> JACS v126 y2006 pp4167-4180

> My set up should have the same charges as in the article.

It's not clear from the commands you give (below) how you got the charges to
be the same as in the article; (those were not the standard Amber charges
for ASP and ASH, I believe).

> The box is generated by the following tleap input:
> logfile logfil
> source leaprc.ff99
> x=loadpdb asph_model.pdb
> solvateOct x TIP3PBOX 9 (or solvateOct x TIP3PBOX 12)
> check x
> saveamberparm x prmtop prmcrd
> quit
>

One check on your setup it to see if you get the same GB results as are
reported for the model compound in section 2 of the tutorial. And, it
certainly is possible that ff94 vs. ff99 could indeed give differences of the
magnitude you report.

...good luck...dac

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