Thanks Jason for reply but I am using Amber10,can I use AmberTools-1.4 with
Amber10.
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
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Received on Wed Jun 09 2010 - 10:30:03 PDT
