![]() * New -num option to print the number of frames in each file, as well * New command line interface: The -o option is now required for * Use of VMD file readers means fixed atoms are handled automatically. To adapt the program to handle other file formats. * Now uses the VMD plugins for file reading. * CatDCD is now integrated into the VMD plugin tree and isĬompiled as part of the standard plugin builds. To use a different compiler or compileįlags, edit the first three definitions in the Makefile. A directory named catdcd will be created.Įnter that directory and type "make". Subsequent frame to eq_first.dcd, until a total of 2000 frames 'protein.ind' from eq01.dcd and writes them to eq_pro.dcdĬatdcd -o eq_first.dcd -first 1000 -last 2000 -stride 10 eq01.dcd eq02.dcdĪfter skipping 999 frames, writes the 1000 frame and every 10th ![]() Takes only the coordinates corresponding to the indices in ![]() Prints the number of frames in the two DCD files, then the total,Ĭatdcd -o eq_all.dcd eq01.dcd eq02.dcd eq03.dcdĬombines eq01.dcd, eq02.dcd, and eq03.dcd into eq_all.dcd.Ĭatdcd -o eq_pro.dcd -i protein.ind eq01.dcd Pretty much anywhere, including non-Unix platforms (I haven't tested this -) The code uses only standard C library commands and should thus be portable to However, they must all have the same number of atoms. The input files may be any combination of charmm or xplor format, and big. stride stride: Specify how many frames to skip when writing. last last: Specify the last frame to write. first first: Specify the first frame to be written to the output file.ĭefault is 1 (write starting from the first frame read). Should be ASCII text, separated by whitespace. Indexfile should contain the (zero-based) indices of the atoms in theĭcd files whose coordinates are to appear in the output file. The number of frames in each file, then exits. num: When present, no output file will be written. Pdb dcd trr crd crdbox namdbin binpos rst7 xyz pqrĬatdcd -o Webpdb cube rst7 tinker dlpolyhist lammpstrj xyz cor molden UniChemXYZ XYZ XED gro g96 trr xtc crd crdbox namdbin binpos Spartan SpartanSE SpartanMM Sybyl Sybyl2 Conjure Maccs2d Maccs3d MopacCartesian MopacInternal MopacOutput PCModel Quanta ShelX Macromodel MicroWorld MM2Input MM2Output MM3 MMADS MDLMOL MOLIN Ĭpmd pdb dcd Alchemy AMBERPREP BallStick BiosymCAR BoogieĬacao CADPAC CHARMm Chem3d-1 Chem3d-2 CSSR FDAT GSTAT Featureįractional GAMESSoutput Z-matrix Gaussianoutput HIN Isis MacMolecule Which frames should be written into the output file thus DCD's can be splitĬatdcd -o outputfile It also allows the user to specify which atoms and catdcd functions much like the Unix "cat" command: it concatenates DCD files * Written by Justin Gullingsrud, based on DCD I/O code from VMD
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