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Home > Error In > Error In Box Coord Line Of Trajectory

Error In Box Coord Line Of Trajectory

Thanks in advance, G.GUENEGOU Next message: maria goranovic: "shades of licorice representation" Previous message: Nicolas Coudray: "RE.: Re: VMD and MDFF: ssrestraints package error message under Windows" Next in thread: John This error message suggests to me that the waterbox information is missing from the solvated complex (n3_new.prmtop) file, yet it is not missing. number of residues" Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ] Custom Search Thank you. -- Ashley Ferraro _______________________________________________ AMBER mailing list Received on Wed Jul 11 2012 - 17:30:04 PDT This message: [ Message body ] Next message: Jason Swails:

Candidate > 352-392-4032 > _______________________________________________ > AMBER mailing list > > > _______________________________________________ > AMBER mailing list > > -- ------------------------- Daniel R. cpptraj returns the same result as Error in box coord line of trajecory Expect only 3 or 6 box coords Problem with line: (line after box coords) To convert the Since // ISIZE = uncompressed % 2^32, // try ((file_size + (2^32 * i)) % frame_size) and see if any are 0. 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.

Now the number of residues in these PDBs are different. The input to driver is specified using the command line arguments described below. Read and set the title and titleSize if ( file_.OpenFile() ) return TRAJIN_ERR; std::string title = file_.GetLine(); // Allocate mem to read in frame (plus REMD header if present). Terms Privacy Security Status Help You can't perform that action at this time.

  • 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
  • Last attempt: I understand that I may write individual frames to disk using the "write" command within an analysis block.
  • OUTPUT TRAJECTORIES: [combined_PPARg_traj.mdcrd.gz] is an AMBER trajectory, Parm 0: Writing 7500 frames ACTIONS: Initializing 0 actions: BEGIN TRAJECTORY PROCESSING: .....................................................
  • The latter will read a file produced by \ref DUMPMASSCHARGE . \par Examples The following command tells plumed to postprocess the trajectory contained in by performing the actions described in

I looked at the trajectories and they seem fine. See the GNU Lesser General Public License for more details. Pharm. Reload to refresh your session.

Skip to content Ignore Learn more Please note that GitHub no longer supports old versions of Firefox. You signed in with another tab or window. Box boxInfo; if ( trajParm->Natom() < 3 ) { mprintf("Warning: Less than 3 atoms, skipping box check.\n"); numBoxCoords_ = 0; } else { std::string nextLine = file_.GetLine(); if ( !nextLine.empty() ) E-mail: _______________________________________________ AMBER mailing list Received on Tue Mar 19 2013 - 01:00:03 PDT This message: [ Message body ] Next message: Albert: "Re: [AMBER] can we

I am trying to do an MMPBSA calculation on my protein > complex. Remember that after patches are applied you need to recompile in order for them to take effect. If not possible and this is not a // compressed file the trajectory is probably corrupted. natom3_ = trajParm->Natom() * 3; file_.SetupFrameBuffer( natom3_, 8, 10, headerSize_, title.size() ); if (debug_ > 0) { mprintf("Each frame is %u bytes", file_.FrameSize()); if (headerSize_ != 0) mprintf(" (including REMD header)");

You need to download the SOURCE of VMD, which contains a plugins directory. But it has given the box error which is strange to me. Locate said file and libmolfile_plugin.h, and customize the configure command with something along the lines of: \verbatim configure [...] LDFLAGS="-ltcl8.5 -L/mypathtomolfilelibrary/ -L/mypathtotcl" CPPFLAGS="-I/mypathtolibmolfile_plugin.h/" \endverbatim and rebuild. Read 7500 frames and processed 7500 frames.

Error: trajin: Could not set up trajectory. No frames defined. Professor, Biochemistry, Molecular Biophysics, and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Thu, May 29, 2014 at 7:03 AM, mahnam karim wrote: > > > > In God For e.g. 1PRG has Glu1-Leu270 and 1FM9 has Pro1-Glu2---TYR271.

if ( (file_size % frame_size) != 0) { // Determine the maximum number of iterations to try based on the // fact that Amber trajectories typically compress about 3x with // amber crd) do not specify atom number. Nothing strange ! > I tried the same trajectories and inputfiles with AmberTools1.4 &Amber11 (earlier I tried the latest versions) > along with solvated complex prmtop file and it works perfectly More about the author unsigned int titleSize = (unsigned int)Title().size() + 1; // +1 for newline titleSize = std::min(81U, titleSize); file_.SetupFrameBuffer( natom3_, 8, 10, headerSize_, titleSize ); file_.ResizeBuffer( numBoxCoords_ ); if (debug_>0) rprintf("'%s'(Parallel): Each frame

Title size is used in seeking. frameBuffer must be large * enough to accomodate all coords in F (handled by SetupWrite). */ // NOTE: The output frame size is calcd here - should it just be precalcd? Swails > Quantum Theory Project, > University of Florida > Ph.D.

Using /usr/local/amber12/bin/sander > mmpbsa_py_energy found!

Can you visualize your files in VMD? All files have been retained. -------------------------------------------------- I went through the previous user lists messages, but there is no clear answers that I could find. Molfile plugin require periodic cell to be triangular (i.e. Here though --trajectory-stride is set equal to the frequency with which frames were output during the trajectory and the --timestep is equal to the simulation timestep.

Personal Open source Business Explore Sign up Sign in Pricing Blog Support Search GitHub This repository Watch 10 Star 15 Fork 14 Amber-MD/cpptraj Code Issues 28 Pull requests 0 Projects Likely cause: either the atom count or the periodic box settings are inconsistent between the two files. if (trajParm->ParmBox().Type() == Box::NOBOX) mprintf("Warning: Trajectory only contains box lengths and topology has no box info.\n" "Warning: To set box angles for topology use the 'parmbox' command.\n"); box[3] = boxAngle_[0] = file_.SeekToFrame( set ); return ( writeFrame(set, frameOut) ); } void Traj_AmberCoord::parallelCloseTraj() { closeTraj(); } #endif Jump to Line Go Contact GitHub API Training Shop Blog About © 2016 GitHub, Inc.

I did not find anything about making a movie of a trajectory using command lines (it is pretty easy with the GUI). Thus. However, it could be false if you rotate the coordinates in your trajectory before reading them in the driver. first vector oriented along x and second vector in xy plane).

sander found! Loading the .top (topology) file gives the following message: ObjectMolecule: Assuming this is an Amber6 topology file. The prmtop file loading is ok (mol new file.prmtop), but concerning the trajectory file (.mdcrd), I do not know how to load it properly. Using /usr/local/amber12/bin/cpptraj > ptraj found!

We recommend upgrading to the latest Safari, Google Chrome, or Firefox. Using /opt/crc/amber/amber12/intel/ bin/mmpbsa_py_energy cpptraj found! Please suggest if you have any idea on how avoid this. numBoxCoords_ = 0; } else if (numBoxCoords_ == 3) { // Box lengths only, ortho.

int Frames = 0; if (debug_>0) rprintf("Title offset=%lu FrameSize=%lu UncompressedFileSize=%lu\n", title.size(), file_.FrameSize(), file_.UncompressedSize()); off_t title_size = (off_t) title.size(); off_t frame_size = (off_t) file_.FrameSize(); off_t uncompressed_size = file_.UncompressedSize(); off_t file_size = uncompressed_size