Hi,
When processing the stripped trajectory you are currently using the
original topology file (3438 atoms), which after stripping no longer
matches (since you now have 2964 atoms in the stripped trajectory).
You need to generate a topology file that matches your output (2964
atom) trajectory.
-Dan
On Mon, Oct 10, 2011 at 1:11 AM, Praapti Jayaswal <praapti.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 10 2011 - 05:30:06 PDT
