Dear All,
My protein has 225 residues. I want to do clustering of the trajectory,
using only a few residues that lie as two different chains in the middle of
the polypeptide. Thus, I tried to strip only specific residues using ptraj
so as to exclude the residues that i do not require, using the following
command :
trajin abc_dry.mdcrd 1 2000 1
center :1-225
strip :1-20
strip :120-130
image center familiar
trajout abc-clust_dry.mdcrd
The output displayed was:
PTRAJ: Processing input from file clust_dry.in
PTRAJ: trajin abc_dry.mdcrd 1 2000 1
Checking coordinates: abc_dry.mdcrd
Rank: 0 Atoms: 3438 FrameSize: 83544 TitleSize: 30 NumBox: 0 Seekable 1
PTRAJ: center :1-225
Mask [:1-225] represents 3438 atoms
PTRAJ: strip :1-20
Mask [:1-20] represents 293 atoms
PTRAJ: strip :120-130
Mask [:120-130] represents 181 atoms
PTRAJ: image center familiar
Mask [*] represents 2964 atoms
PTRAJ: trajout abc-clust_dry.mdcrd
abc_dry.mdcrd: 2000 frames.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 2000 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (abc_dry.mdcrd) is an AMBER trajectory with 2000 sets
OUTPUT COORDINATE FILE
File (abc-clust_dry.mdcrd) is an AMBER trajectory
ACTIONS
1> CENTER to box center via center of geometry, atom selection follows
* (All atoms are selected)
2> STRIP: 293 atoms will be removed from trajectory: :1-20
3> STRIP: 181 atoms will be removed from trajectory: :120-130
4> IMAGE familiar by molecule to box center using the center of mass,
atom selection * (All atoms are selected)
IMAGE familiar, center is at box center
Processing AMBER trajectory file abc_dry.mdcrd
1% ............ 25% ............ 50% ............ 75% ............ 100%
PTRAJ: Successfully read in 2000 sets and processed 2000 sets.
Dumping accumulated results (if any)
This output trajectory, abc-clust_dry.mdcrd, when read in by ptraj to
perform clustering, contains 1722 frames, instead of the original 2000
frames. The following output was displayed:
PTRAJ: Processing input from file ptraj_clustering.in
PTRAJ: trajin abc-clust_dry.mdcrd 1 2000 1
Checking coordinates: abc-clust_dry.mdcrd
checkCoordinates(): Could not predict number of frames for AMBER trajectory
file: jfq-clust_dry.mdcrd
If this is not a compressed file then there is a problem
Rank: 0 Atoms: 3438 FrameSize: 83609 TitleSize: 30 NumBox: 8 Seekable 0
PTRAJ: cluster out abc-cluster representative pdb averagelinkage clusters
500 rms
MASK = (null)
Mask [*] represents 3438 atoms
[No output trajectory specified (trajout)]
abc-clust_dry.mdcrd: 1722 frames.
How do you suggest I avoid losing frames?
Is it possible to strip only specific residues that i do not require,
without the loss of frames?
Thanks,
Praapti
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Received on Sun Oct 09 2011 - 22:30:03 PDT
