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
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Received on Wed Mar 26 2014 - 07:30:03 PDT
