AMBER Archive (2009)

Subject: Re: [AMBER] some queries on -states flag in constant pH simulation

From: nicholus bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Sat Oct 31 2009 - 01:31:31 CDT

On Fri, Oct 30, 2009 at 9:00 AM, Jason Swails <jason.swails_at_gmail.com>wrote:

> Nicholus,
>
> This will only define the protonation state of the titratable residues.
> The
> titratable residues are those which you specify when you create the CPIN.
> If you do not specify which residues to make titratable when you create the
> CPIN file, then it will choose all residues with the names GL4, AS4, HIP,
> and LYS. You should be able to tell which residues are titratable by
> looking at the cpin file, as there is an array that specifies the residue
> name, and also the residue number.
>
> It is generally OK to use the default initial protonation states. However,
> if it is obvious that two carboxylates are involved in an H-bond bridge, or
> something similar to that, just by looking at the crystal structure, you
> may
> want to protonate one of those residues (since not protonating will
> introduce an unfavorable interaction). However, even this is probably not
> crucial if you relax your system carefully.
>
> Before you do get started with your actual simulations, however, I would
> advise that you apply the constant pH bugfix found on the amber website if
> you haven't already. There are instructions on how to apply it on the
> website.
>
> Good luck!
> Jason
>
> On Fri, Oct 30, 2009 at 12:21 AM, nicholus bhattacharjee <
> nicholusbhattacharjee_at_gmail.com> wrote:
>
> > Dear community,
> > The -states flag is used to define the initial
> > protonated states of the residues. My queries are asfollows
> >
> > 1. Is this flag used only to define protonated states of titratable
> > residues
> > or all the residues in the protein sequence?
> >
> > 2. Which are the titratable residues?
> >
> > 3. Is it ok to use the default initial protonation states or we have to
> > specify them? If we have to specify them than how do we know which
> > protonation states to be specified to which residue?
> >
> >
> > --
> > Nicholus Bhattacharjee
> > PhD Scholar
> > Department of Chemistry
> > University of Delhi
> > Delhi-110007 (INDIA)
> > Phone: 9873098743(M)
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

I have done the bug fix with bugfix.all patch file for amber 9. Hope this
should be OK. 

-- 
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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