Hi again,
Ptraj is a program that is part of AmberTools, not amber10. You may well
have AmberTools1.2 installed if you're running amber10 (perhaps you used
leap to get your prmtop & inpcrd files - tleap/xleap is also an AmberTools
program). If not, you can install it.
You can read the AmberTools1.2 manual to find out how ptraj can read in
trajectory files and calculate RMSD.
Hope this helps,
Marc
On Wednesday, 25 January 2012, Atila Petrosian <atila.petrosian.gmail.com>
wrote:
> Dear Marc van der Kamp
>
> Thanks for your quick reply.
>
> you are right : 2) 200 ps equilibration (NVT).
>
> There is not cpptraj in amber 10 manual.
>
> please explain more.
>
> On 1/25/12, Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
>> Read the AmberTools manual. Ptraj (& cpptraj) can read in trajectory
files
>> and calculate RMSD.
>> Marc
>> PS are you not doing NVT in your first equilibration / heating step?
>> On 25 Jan 2012 10:45, "Atila Petrosian" <atila.petrosian.gmail.com>
wrote:
>>
>>> Dear amber users
>>>
>>> I did md simulation of protein as follows:
>>>
>>> 1) minimization
>>>
>>> 2) 200 ps equilibration (NPT)
>>>
>>> 3) 300 ps equilibration (NPT)
>>>
>>> 4) 1000 ps production run (NPT)
>>>
>>> In analysis step, I want to obtain RMSD in all of the simulation time
>>> (200+300+1000 = 1500 ps)
>>>
>>> how to do that?
>>>
>>> any help will highly appreciated.
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
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>>
>
>
> --
> Atila Petrosian
> Ph.D. student of BioPhysical Chemistry
> University of Oulu,Finland
>
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>
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Received on Wed Jan 25 2012 - 04:30:03 PST
