Respected sir,
Thanks for prompt reply and yes that solved my problem. Only one more query regarding generation of stripped prmtop. As I can generate the prmtop files by following two which I can see differs slightly in their size. So, which process is the correct approach?
cpptraj complex_solvated.prmtop strip2merge_2 > strip2merge_2.out
#strip2merge2
trajin 5md.mdcrd 2000 last
strip :1-18,168-182,Na+,Cl- outprefix stripped_2NL9_046
trajout 2NL9_046_strip.mdcrd netcdf nobox
OR
parmed.py complex_solvated.prmtop strip_Parm_2
#strip_Param_2
strip :1-18,168-182,Na+,Cl- outprefix stripped_2NL9_046
parmout /hpctmp/a0068362/MCL1_combined_test/2NL9_046_strip_prmtop.prmtop
Moreover, as prmtop file is required by cpptraj so do I need to load both prmtop files or have to merge prmtop files as well. If I have to merge them then how can I do that ?
Thanks and regards,
Nitin Sharma
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Wednesday, March 26, 2014 10:27 PM
To: amber.ambermd.org
Subject: Re: [AMBER] combining trajectories with diff. number of residues for same protein
On Wed, 2014-03-26 at 21:29 +0800, Nitin Sharma wrote:
> Dear amber users,
>
> I have two different PDB structures for same protein and 50 ns
> trajectory for each. Now I want to merge these two trajectories but
> terminal residues are different in two PDB files.
>
> I stripped the trajectory files using following commands:
>
> cpptraj complex_solvated.prmtop strip2merge_1 > strip2merge_1.out
> #strip2merge1
> parm complex_solvated.prmtop
This "parm" command is unnecessary. The first argument in cpptraj loads the topology file.
> trajin 5md.mdcrd 2000 last
> strip :1,151-154,Na+,Cl- outprefix stripped_4HW4_046 trajout
> 4hw4_046_strip.mdcrd netcdf nobox
>
> cpptraj complex_solvated.prmtop strip2merge_2 > strip2merge_2.out
> #strip2merge2
> parm complex_solvated.prmtop
Same with this parm command.
> trajin 5md.mdcrd 2000 last
> strip :1-18,168-182,Na+,Cl- outprefix stripped_2NL9_046 trajout
> 2NL9_046_strip.mdcrd netcdf nobox
>
> this gave me stripped .mdcrd and .prmtop files. Then I tried to
> combined both by using following command
>
> cpptraj combine_trajectory > combine_trajectory.out
Use "cpptraj -h" to get the full usage. If you do not use any command-line flags (like "-i" or "-p") to specify whether the files are input scripts or topology files, then cpptraj will revert to the default ptraj behavior. Namely:
cpptraj <Top> <Input>
As a result, it is interpreting "combined_trajectory" as a topology file when it is really an input script.
Change your command to
cpptraj -i combined_trajectory > combine_trajectory.out
instead.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
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 Wed Mar 26 2014 - 11:00:04 PDT
