Thanks for suggestion,i have solved my problem.
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Thu Jun 10 2010 - 08:30:05 PDT
