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.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.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
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Received on Fri Oct 30 2009 - 06:30:06 PDT
