AMBER Archive (2009)

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

From: Jason Swails (jason.swails_at_gmail.com)
Date: Sat Oct 31 2009 - 07:28:22 CDT

This will be OK as long as you downloaded and applied bugfix.all after Sept.
1 of this year. The reason I brought it up was because it was a very recent
bug fix.

All the best!
Jason

On Sat, Oct 31, 2009 at 2:31 AM, nicholus bhattacharjee <
nicholusbhattacharjee_at_gmail.com> wrote:

> 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)
> _______________________________________________
> 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