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
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
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
# combine_trajectory
parm stripped_4HW4_046_complex_solvated.prmtop [4hw4]
trajin 4hw4_046_strip.mdcrd parm [4hw4]
parm stripped_2NL9_046_complex_solvated.prmtop [2NL9]
trajin 2NL9_046_strip.mdcrd parm [2NL9]
outprefix combined_2NL9_4HW4_046
trajout combined_2NL9_4HW4_046.mdcrd
BUT it showed error
Error: Read: Format of parm [combine_trajectory] not recognized.
Error: Could not open parm combine_trajectory
Then I generated stripped prmtop using ParmEd by following command
parmed.py complex_solvated.prmtop strip_Parm_1
#strip_Param_1
strip :1,151-154,Na+,Cl- outprefix stripped_4HW4_046
parmout /hpctmp/a0068362/MCL1_combined_test/4hw4_046_strip_prmtop.prmtop
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
and tried to merge files like dope previously BUT got same error.
Can anyone tell what I am missing here?
Regards,
Nitin Sharma
Department of Pharmacy,Faculty of Science,National University of Singapore,block S7, Level 2, Singapore : sharmanitin.nus.edu.sg<mailto:sharmanitin.nus.edu.sg> ; http://www.linkedin.com/in/imsharmanitin
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Received on Wed Mar 26 2014 - 07:00:03 PDT
