On Wed, Jun 9, 2010 at 1:06 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
> Thanks Jason for reply but I am using Amber10,can I use AmberTools-1.4 with
> Amber10.
>
You can use AmberTools 1.4 to create the topology file, which is all that's
needed to run constant pH MD. Defining a "titratable site" only involves
protonating every possible site. HIP is the definition of a Histidine that
is protonated in both the delta and epsilon position. AS4 and GL4 are
aspartate and glutamate residues with 4 defined protons (syn and anti on
both oxygens). LYS has every proton (as opposed to LYN, which is neutral),
and TYR has the proton as well.
Hope this helps,
Jason
> Here is one more query, in Amber10 for constant pH MD simulation there is
> requirement for PDB file editing and it is define for:
>
> (HIS, HID, or HIE) with HIP, ASP and ASH to AS4 and all GLU and GLH to
> GL4.
>
> But not for LYS and TYR and in manual it has witten that:
>
> Amber provides deļ¬nitions for titrating side chains of ASP, GLU, HIS, LYS
> and
> TYR.
>
> Is there not requirement for editing of PDB for LYS and TYR?
>
>
>
> > Hello,
> >
> > This file does not exist. It is the basis for the ff99SB force field
> > modifications as I understand it. You have a couple options. If you're
> > using tleap from AmberTools-1.4, a new constant pH leaprc file has been
> > created to automate all of these commands. Thus, all you have to do is
> > enter the command
> >
> > source leaprc.constph
> >
> > This will load constant pH parameters. This will, by default, load the
> > constant pH library with GL4 and AS4, as well as the frcmod.constph, and
> > change the default pbradii to mbondi2, as needed for constant pH
> > simulations.
> >
> > This file executes the following commands in your leap session:
> >
> > source leaprc.ff99SB
> > loadamberparams frcmod.constph
> > loadoff constph.lib
> > set default pbradii mbondi2
> >
> > If you don't use the leaprc.constph, then execute the above commands.
> The
> > instructions for starting constant pH simulations has been updated to use
> > leaprc.constph in the Amber11 manual, but it's still available for
> Amber10
> > through AmberTools 1.4.
> >
> > Hope this helps,
> > Jason
> >
> > On Wed, Jun 9, 2010 at 11:13 AM, Sangita Kachhap <sangita.imtech.res.in
> >wrote:
> >
> >>
> >> Hello all
> >>
> >> I have to do constant pH MD simulation using amber10 for this there is
> >> requirement of a file:
> >> frcmod.mod_phipsi.1
> >> But in amber10 there is no such any file.
> >>
> >> >From where i can get this file?
> >>
> >> There are option for editing PDB file for (HIS, HID, or HIE) with HIP,
> >> ASP and ASH to AS4 and all GLU and GLH to GL4, but there are no any
> option
> >> to
> >> change for
> >> LYS and TYR before preparation of prmtop and prmcrd file for constant
> pH
> >> MD
> >> simulation.
> >>
> >> Is there no need to change them or there are some other option?
> >>
> >> With regard
> >> Sangita Kachhap
> >> JRF
> >> BIC,IMTECH
> >> CHANDIGARH
> >>
> >> _______________________________________________
> >> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
> _______________________________________________
> 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 Wed Jun 09 2010 - 11:00:03 PDT
