A couple comments here. Belly is *supposed* to keep the mask that is NOT
part of the belly completely fixed (by actually zeroing out the force and
everything). The restraint method is probably the preferred way of doing
things in this case, but know that in this case the atoms CAN move a little.
You can easily calculate the penalty involved in moving the atoms a given
distance from their starting positions. A constraint of 500
kcal/mol/Angstrom ** 2 is quite strong, and will incur a 500 kcal/mol energy
penalty on any atom that deviates 1 angstrom from its reference position.
For minimization this is fine, but just keep in mind that if you want to
hold your system completely fixed during dynamics, belly may be the better
way to go, since a very high harmonic restraint constant (i.e., 500
kcal/mol/Angstrom ** 2) requires a smaller time step.
Hope this helps,
Jason
On Wed, Mar 23, 2011 at 2:28 PM, Haldoupis I. <ih2g09.soton.ac.uk> wrote:
> Hi Per,
>
> Thanks for your quick reply. Hopefully it will work.
>
> Best Regards,
> Ioannis
>
>
> ________________________________________
> From: Per Jr. Greisen [pgreisen.gmail.com]
> Sent: 23 March 2011 20:14
> To: AMBER Mailing List
> Subject: Re: [AMBER] how to minimize a protein-ligand system with the
> protein constrained
>
> Hi
>
> Keep ntr=1 and then add the following lines to your md-input file
>
> /
> Hold protein fixed
> 500.0
> RES 1 100
> END
> END
>
> RES is the number of residues in your protein - here is given an
> example of 100. 500 is the weight and that should keep your protein
> fixed.
>
> With kind regards,
>
> On Wed, Mar 23, 2011 at 9:09 PM, I.Haldoupis <ih2g09.soton.ac.uk> wrote:
> > Dear Amber users,
> >
> > I am a new user and I need to initially perform a minimization of my
> > protein-ligand system keeping the protein rigid.
> >
> > I have seen in the tutorials and the manual that there are different
> > ways one can restrain atoms: the command ntr with restraint_wt and
> > restraintmask; ibelly with bellymask ( I will be performing that in GB
> > solvent i.e. igb>0 so I am not sure if this option is available); Belly
> > Group; Group Input (as in tutorialB1: Simulating a small fragment of DNA
> > section 5.1.3.
> >
> > However, is there a method that can keep the protein completely frozen?
> > Would placing a very high restraint weight achieve that?
> >
> > Has anyone faced a similar issue?
> >
> > Best wishes,
> > Ioannis.
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Per
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Mar 23 2011 - 18:00:03 PDT
