AMBER Archive (2009)

Subject: Re: [AMBER] constant-pH: appearance of not titrated residues during the Monte Carlo simulation

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Apr 04 2009 - 08:20:28 CDT

On Wed, Apr 01, 2009, Therese Malliavin wrote:
>
> c) Do you have some experience about the right cutoff value to use to
> run a stable constant-pH simulation? Does a cutoff of 30 A mandatory? I
> am asking the question because the large cutoff have an impact on the
> duration of the run... ;-)

Thirty angstroms is conservative; a value of 15-20 should work,
especially if you are using a non-zero salt concentration. Of course,
it can be hard to detect subtle biasses that arise from cutoffs, so
always be careful.

> RESNAME='System: Unknown','Residue: AS4 132','Residue: GL4 173',
> 'Residue: AS4 174','Residue: GL4 177','Residue: AS4 278','Residue: GL4 291',
> 'Residue: GL4 334',

The first entry in the RESNAME array looks odd -- does that give you any
clues?

> RESSTATE = 0, 2*3, 2*1, 0, 2, 2*0, 1, 40*0,

Note that the sum of the RESSTATE values is 9, so I'm guessing that that
the "Residue 9" might refer to states(?). Just guessing, though.

....good luck...dac

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber