Re: [AMBER] correct syntax for assinging scmask to two atoms of different molecules

From: <>
Date: Thu, 1 Apr 2010 10:14:04 -0400 (EDT)


if you are changing a N into C, you probably dont need to use soft core
potentials, since the atoms are approximately the same size (You could
leave them both in the scmasks if you want, but the end results should be
almost the same).

The error you see probably means that not all atoms in your V0 and V1 rst
files are at the same coordinates (sander adjusts small deviations from
i.e. recentering the box, but not really different positions). Your prmtop
files (except for the atoms that actually appear or disappear) need to be
identical with respect to number and starting positions of all particles.

I would not recommend changing a charge on a ligand *and* changing the
number of ions simulatiously. Leave out the ion on both sides and run your
system with an imbalanced charge (e.g. q(V0)=1 -> q(V1)=0), sander will
correct for this.

'What about the ion-water interaction?' you may ask, but that will cancel
out in your second leg of the TI run, when you change e.g. your ligand in
water. Neglecting the change in ion numbers will happen on both
transformations and have the same effect on dG, unless you have good
evidence that the charged ligand binds to the protein together with an

Kind Regards,


On Thu, April 1, 2010 10:00 am, imtiaz shafiq wrote:
> I want to learn the correct syntax how to assign scmask for two atoms
> on two different molecules.
> I can assign scmask to one atome on one molecule like this
> scmask=':LIG.H2',
> Please help me how to assign scmask if I have more than one atome.
> Please also suggest how I can assign scmask to Cl- ions in the protein
> If my protein complex change a charge during the transition
> Regards
> Imtiaz
> _______________________________________________
> AMBER mailing list

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

AMBER mailing list
Received on Thu Apr 01 2010 - 07:30:05 PDT
Custom Search