Thank you, Dan.
The ambertools version I am using is 1.4. Amberversion is 11.
1. For extract trajectories without combine the mdcrd file:
trajin ../SLT1_CnsP_1ns.mdcrd
trajin ../SLT1_CnsP_2ns.mdcrd
trajin ../SLT1_CnsP_4ns.mdcrd
trajin ../SLT1_CnsP_4ns_c.mdcrd
......
trajin ../SLT1_CnsP_50ns.mdcrd
trajin ../SLT1_CnsP_55ns.mdcrd
trajin ../SLT1_CnsP_60ns.mdcrd
strip :WAT
average SLT1_Dyn_Avg_Str_60ns.pdb start 1500 pdb
trajout ./Traj/SLT1_Dyn PDB offset 50
2. Combine mdcrd files and extract trajectories:
-------------
trajin ../SLT1_CnsP_1ns.mdcrd
trajin ../SLT1_CnsP_2ns.mdcrd
trajin ../SLT1_CnsP_4ns.mdcrd
trajin ../SLT1_CnsP_4ns_c.mdcrd
......
trajin ../SLT1_CnsP_50ns.mdcrd
trajin ../SLT1_CnsP_55ns.mdcrd
trajin ../SLT1_CnsP_60ns.mdcrd
strip :WAT
rms first name .CA
trajout ./Prepare/SLT1_Dyn_60ns_rm_Cl_rms.mdcrd trajectory
average ./Prepare/SLT1_1_60ns_avg.pdb PDB
go
---------
trajin ./Prepare/SLT1_Dyn_60ns_rm_Cl_rms.mdcrd
trajout ./Traj/SLT1_Dyn_60ns_rms PDB
go
----------
With this way, from about 48ns, the structure showed weird bond
connections. But when I did this to individual mdcrd file, all the
structure were right:
--------
trajin ../SLT1_CnsP_50ns.mdcrd
strip :WAT
rms first name .CA
trajout ./Prepare/SLT1_Dyn_45_50ns_rms.mdcrd trajectory
go
--------
trajin ./Prepare/SLT1_Dyn_45_50ns_rms.mdcrd
trajout ./Traj_45_50/SLT1_Dyn_From45ns_rms PDB
go
-------
Hope this can explain what I did.
Thanks,
William
On 1/20/12, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I'm having a lot of trouble understanding your exact issue. It will
> help if you can post the exact ptraj input you are using that doesn't
> work for you. Also, what is the version number of the older ptraj you
> say works, and what is the version number of the new version you say
> doesnt work?
>
> -Dan
>
> On Fri, Jan 20, 2012 at 10:25 AM, Lianhu Wei <lianhu.wei.gmail.com> wrote:
>> Hi All,
>>
>> I have performed MD simulation for a protein in water for 60ns. With
>> older version I cam trajin all these file, then trajout the
>> trajectories in order, but with new version, the trajectories from
>> second mdcrd file will use the name as the first sets (prefix.number,
>> the number start from 1 again). So it replaced the trajectories from
>> the first mdcrd. So the trajectories I got is only the last set from
>> the last mdcrd file. Is there a solution for this?
>>
>> I tried to remove water and combined those trajectory to one file.
>> The I extract the trajectories from the combined file. But from about
>> 48ns, the structure got wield bond connection. I tried to extract
>> from the uncombined mdcrd files using the same procedure, the
>> trajectories are all okay. Does any had this problem? Is there any
>> clue for this?
>>
>> Thanks,
>> William
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Postdoctoral Associate
> BioMaPS Institute, Rutgers University
> 610 Taylor Road
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 20 2012 - 09:30:03 PST
