Dear Amber community members,
I have trajectory files for a protein generated from different PDB files
with different number of residues.
For e.g. I have structure 1PRG with residues 1-270 and 2PRG with residues
1-271 (272 is ligand).
Now I want to plot rmsd between trajectory of 2PRG and reference structure
(PDB generate with ambpdb) of 1PRG.
I am following the below mentioned procedure, but I'm not sure if the
results are meaningful (rmsd > 500 ?). Ptraj also gives warning that
expected and actual number of atoms are different.
*Please suggest me how can I use two prmtop for different trajectories
together to get the rmsd between two trajectories of same protein but with
different number of residues (hence different sequence).*
Step 1. ptraj 2PRG.prmtop < 2PRG_new_traj.in
ptraj input file for step 1.
2PRG_new_traj.in
------------
trajin 2PRG.mdcrd
strip :271
trajout 2PRG_new.mdcrd
-----------
Step 2. Then I have generated prmtop for 2PRG with residue 271 deleted
(2PRG_new.prmtop)
Step 3. ptraj 2PRG_new.prmtop < 2PRG_1PRG.in
ptraj input file for step 3.
2PRG_1PRG.in
---------
trajin 2PRG_new.mdcrd
rms reference 1PRG.pdb out 2PRG_1PRG.rmsd :1-271.CA,C,N,O
--------
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Mon Dec 03 2012 - 03:30:02 PST
