Dear Amber community members,
I wish to combine trajectories from the simulation of various PDB's. Now
the number of residues in these PDBs are different. For e.g. 1PRG has
Glu1-Leu270 and 1FM9 has Pro1-Glu2---TYR271. Thus. I tried to combine all
the trajectories into one file using following procedure. But it not
successful, please suggest how can I modify the trajectories and associated
prmtops to generate one long MD trajectory which can be analyzed using
appropriate prmtop.
1) I used cpptraj input files like give below to strip atoms that are not
common to 1PRG structure. This wrote a trajectory which has atoms identical
to 1PRG for 1FM9 as an example.
FGZ_prostraj.in
-------
parm /home/gm/Documents/MD/100ns_MD_inputfiles/1FM9_FGZ_VAC.prmtop [FGZ]
trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/1FM9_FGZ_md_100ns_VAC.mdcrd.gz
2501 5000 1 [FGZ]
trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/1FM9_FGZ_md_101-200ns_VAC.mdcrd.gz
[FGZ]
strip :1,272
trajout
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_prostraj.mdcrd.gz
nobox
--------
2) Then I Generated prmtop for new FGZ trajectory using following parmed.py
script and commands
command:
parmed.py ../100ns_MD_inputfiles/1FM9_FGZ_VAC.prmtop FGZ_parm.in
FGZ_parm.in file:
--------
strip :1,272
parmout
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_VAC_prosparm.prmtop
------
This has written a smaller prmtop file for new 1FM9 trajectory.
3) Then I generated a combined trajectory for 1PRG without box information
(to avoid box error, but the error is still there).
parm /home/gm/Documents/MD/100ns_MD_inputfiles/1PRG_VAC.prmtop [1PRG]
trajin /home/gm/Documents/MD/100ns_MDoutputfiles/1PRG_md_100ns_VAC.mdcrd.gz
2501 5000 1 [1PRG]
trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/1PRG_md_101-200ns_VAC.mdcrd.gz
[1PRG]
trajout
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1PRG_prostraj.mdcrd.gz
nobox
4) Then I used these newly generated trajectories for 1FM9 along with
trajectories for 1PRG for making a sample combined trajectory using the
cpptraj input file given below. But it has given the box error which is
strange to me. Please suggest if you have any idea on how avoid this.
combined_traj1.in file used in the command below:
-----
parm /home/gm/Documents/MD/100ns_MD_inputfiles/1PRG_VAC.prmtop [1PRG]
parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_VAC_prosparm.prmtop
[FGZ]
trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1PRG_prostraj.mdcrd.gz
trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_prostraj.mdcrd.gz
[FGZ]
trajout combined_PPARg_traj.mdcrd.gz nobox
----
gm.linux-rfml:~/Documents/MD/100ns_MDoutputfiles/processed_trajs> cpptraj
-i combined_traj1.in
CPPTRAJ: Trajectory Analysis. V12.1
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from file combined_traj1.in
[parm /home/gm/Documents/MD/100ns_MD_inputfiles/1PRG_VAC.prmtop [1PRG]]
[parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_VAC_prosparm.prmtop
[FGZ]]
[trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1PRG_prostraj.mdcrd.gz]
[1PRG_prostraj.mdcrd.gz] contains 7500 frames.
[trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_prostraj.mdcrd.gz
[FGZ]]
Error in box coord line of trajectory
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_prostraj.mdcrd.gz.
Expect only 3 or 6 box coords.
Problem line: 2.496 -10.136 -6.735 2.908 -10.111 -8.037 2.577
Error: Could not set up
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_prostraj.mdcrd.gz
for reading.
Error: trajin: Could not set up trajectory.
[trajout combined_PPARg_traj.mdcrd.gz nobox]
INPUT TRAJECTORIES:
[1PRG_prostraj.mdcrd.gz] is an AMBER trajectory, Parm 0 (reading 7500 of
7500)
Coordinate processing will occur on 7500 frames.
PARAMETER FILES:
0: [1PRG], 4401 atoms, 270 res, no box, 7500 frames
1: [FGZ], 4468 atoms, 271 res, no box
REFERENCE COORDS:
No reference coordinates.
No frames defined.
OUTPUT TRAJECTORIES:
[combined_PPARg_traj.mdcrd.gz] is an AMBER trajectory, Parm 0: Writing
7500 frames
ACTIONS: Initializing 0 actions:
BEGIN TRAJECTORY PROCESSING:
.....................................................
PARM [1PRG_VAC.prmtop]: Setting up 0 actions.
----- [1PRG_prostraj.mdcrd.gz] (1-7500, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 7500 frames and processed 7500 frames.
ACTION OUTPUT:
DATASETS:
There are no data sets set up for analysis.
--
With regards
Vaibhav A. Dixit
Ph.D.
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, +91-7709129400.
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Tue Mar 19 2013 - 01:00:03 PDT
