Download charm topology file

Converts AMBER topology and coordinate files to GROMACS format. Perturbation calculations are supported. Experimental support of TINKER format. Tested on numerous molecules (incl. DNA hexamer with ligand) with energy difference between AMBER and GROMACS less than 0.01%. Uploaded 02:59 November 30, 2002 by Filip Ryjacek (ryjacek@msn.com)

Moved from Joomla, there were no comments about this file.

This script calculates the entropies from the output of g_covar by applying the quasiharmonic approximation. See details inside. Was tested on GMX 3.2.1 only. A script for GMX 3.1.4 is available from the author.

Chandran is a tool to make a ramachandran plot colored by occupancy. It reads rama.xvg and produces rama.xpm which can be converted to ps with xpm2ps. Uploaded 12:29 October 09, 2002 by Marcos Villarreal (arloa@dqb.fcq.unc.edu.ar)

A script to convert charmm topology files to gromacs. It has been tested recently with CGenFF files and seems to work. Check the output carefully before using.

Two perl scripts intended to facilitate calculations using GROMACS programs and CHARMM forcefields. These are both considered alpha-release - users should verify the accuracy of their performance by comparing energy evaluations on the same structures in CHARMM and GROMACS. convert_charmm_to_gromacs.pl takes a CHARMM force field file as input and produces ffcharmmbon.itp and ffcharmmnb.itp which when placed in the GMXLIB directory allow pdb2gmx to accept a "-ff charmm" flag and produce an approximation to a CHARMM .top file. This approximation is not normally useful, because pdb2gmx does not natively create Urey-Bradley interactions where they are used by CHARMM, nor does it readily use the 1-4 LJ parameters that differ from the normal LJ parameters for some atom types, nor can it generate multiple periodic dihedral functions such as CHARMM uses for some dihedrals - these must be converted to Ryckaert-Bellemans functions, i.e. expressed as a cosine power expansion. fix_top_for_charmm.pl takes the .top file produced by pdb2gmx, runs grompp on it and notices each occurence of the above three types of error and fixes them, outputing a new .top file that the user can keep and use themselves as input to grompp at their convenience. The advantage of making available the conversion program, rather than the just the results is that it will be easy to use convert different versions of CHARMM force fields, or modified versions so long as the .prm format stays the same. Also my algorithms can be checked, and corrected if necessary. No attempt is made to convert the CHARMM residue toplogies - please consult those of Yuguang Mu at http://www.gromacs.org/old/topologies/uploaded_force_fields/charmm_gromacs.tar.gz in the first instance. Both scripts are released under the GNU General Public License.

This scripts takes an alignment in FASTA format and generates comands for make_ndx. the ndx files created with that commands allows g_confrms to superimpose the structures corresponding to the aligned sequences, even if they don't have the same number of aminoacids (only the aligned aminoacids in the FASTA file will be superimposed)

This is a program to convert GROMOS96 formatted topology, and conformation files to their GROMACS equivalents. Uploaded 19:41 January 10, 2003 by Claudio M. Soares (claudio@itqb.unl.pt)

Solaris\' csh has trouble with exclamation points at the end of strings; this patch removes the troublesome !\'s in the gromacs demo. Uploaded 04:33 April 15, 2002 by Nathan Sharfi (nisharfi@csupomona.edu)

do_multiprot reads a trajectory file and aligns it to a reference structure each time frame calling the multiprot program. This allows you to use a reference structure whose sequence is different than that of the protein in the trajectory, since the alignment is based on the geometry, not sequence. The output of do_multiprot includes the rmsd and the number of residues on which it was calculated. To use do_multiprot, you must have the multiprot program itself. For information about multiprot (and how to get it), see: http://bioinfo3d.cs.tau.ac.il/MultiProt to use do_multiprot 1. Unpack archive tar -xzvf do_multiprot.tgz this yield the directory do_multiprot_dist You must also make sure that you have gromacs and multiprot installed. 2. >cd [location] where location is the full path to do_multiprot_src directory 3. get the information from the README and INSTALL files

dock is a Perl script to perform MD simulations with Gromacs in different flavours. Specially designed to study Proteins and Protein/Ligand interactions, it automates several common steps like Energy Minimization and Position Restraints before MD step. In addition, it is able to restart a simulation after a crash in a very easy way. Files are organized in subdirectories separating data files from result files and using uniform file names. In addition, it can deal with PRODRG topology files allowing the study of complexes between proteins and arbitrary ligands.

ego2xtc will convert trajectories generated by the EGO simulation software (multiple .ego files) to the .xtc trajectory format. This allows EGO trajectories to be analysed by the gromacs analysis and trajectory conversion tools AND saves a large amount of disk space. (package contains both source code and binaries for DEC, SGI and linux) Uploaded 08:49 December 02, 2002 by Bert de Groot (bgroot@gwdg.de)

General Information: ------------------- This package contains a modified version of g_covar, which can print a matrix of atomic correlation coefficients (with -xpmc) and write all pairs with a correlation > 0.5 to a log file (with -clog). Otherwise it is the same as the original program. The xpm correlation matrix shows only cross-correlations larger than 0.5 (absolute values) on the upper triangle and all values on the lower triangle. Thus, the upper triangle displays only the most correlated motions.

Using the -sort option to mdrun greatly increases scaling efficiency (100% to 4cpu). g_desort is then required to deshuffle and desort the trajectory file, thereby recovering full trajectory information. This is not recommended for beginner gromacs users. Users are encouraged to test their results before committing to long runs.

g_puckering computes the Cremer-Pople-Puckeing Parameters of Pyranoses and Hexanoses. Homepage: http://oc24.uni-paderborn.de/~revilo/en/g_puckering.html - Version for Gromacs 3.3.x

g_puckering computes the Cremer-Pople-Puckeing Parameters of Pyranoses and Hexanoses. Homepage: http://oc24.uni-paderborn.de/~revilo/en/g_puckering.html - Version for Gromacs 4.0.x

This is a program to calculate the rdf with COM. This program is based on the original of the g_rdf.c and the work of Jochen Hub. As default, the structure center is calculated. One can calculate the center of mass by opening line 394 and closing line 393. The -com_rdf -o and the -com_rdf -cn are tested. If one wants to calculate other parameters, please use the original g_rdf.c.

g_sdf calculates the spatial distribution function (SDF) of a set of atoms relative to a reference molecule. Output is aN isosurface file in plt format, readable by gOpenMol and VMD. Written by Christoph Freudenberger, with modification by Tsjerk Wassenaar to work with 3.3.1.

g_spatial calculates the spatial distribution function and outputs it in a form that can be read by VMD as Gaussian98 cube format. This program differs from g_sdf in that it gives the user full control of the alignment procedure. The downside is that it requires more time and more disk space.

Here is a script that will run a Galactic dynamics simulation. The system provides 1 black (darjk grey) hole, some stars, some planets and some comets, all under the influence of gravity only. Please hack the script as you like. You will need the latest CVS version of GROMACS (from today!) in order to bypass a check in grompp for negative epsilon_r. If you ish you can also comment out the check in readir.c, it will not influence your normal simulations.

This is a patch to addconf.c, in the tools directory, which improves the --maxsol option to genbox (which limits the number of solvent molecules added). The maxsol option works by removing some of the solvent molecules that have already been added; this patch targets solvent molecules that are at the edges of the box to be removed first. It applies to GROMACS 3.3.2, and probably to 3.3.3, but I have not tested this yet. Homepage: http://cesario.rutgers.edu/easmith/research/

This is a modification to the genbox program that improves the maxsol option, by first removing atoms that are at the edges of the box before going on to do any further removals using the existing methodology. See the README file for more. -Allen Smith, Ph.D. http://cesario.rutgers.edu/easmith/research/

GIMLi-1.0: GROMACS Including Monte Carlo Mutation Moves for Mixtures of Lipids (not official GROMACS!) The purpose of this modified version of Gromacs 3.3.1 is to perform an isomolar semi-grand canonical ensemble (constant N,∆µ,T – depending on settings, can be also constant p,γ or A) simulation of a mixture of 2 lipid types with different tail structures. Why would you want to do this? To achieve an equilibrated lateral distribution of the lipids in your mixture (potentially) much faster than you can by waiting for your lipids to diffuse around your system and sample different arrangements. This can be particularly interesting if there are different microenvironments in your system, determined by proximity to a membrane protein or other perturbation to the bilayer. Homepage: http://www.chemistry.emory.edu/faculty/kindt/

This contribution is for GROMACS users who experience poor parallel scaling with PME on Ethernet connected clusters. It consists of 1.) a program to test if there are TCP packet drops during MPI_Alltoall communication on your cluster 2.) a patch for gromacs 3.3.1 that incorporates an optimised all-to-all algorithm to reduce packet loss

This is a utility to rescue partly corrupted XTC files. It works under Linux and is based on earlier files contributed for SGI (see README.rescue) The actual files are called gmx_rescue.c and README.rescue. It came in handy for me because a lot of simulations that I had run on some supercomputer had corrupted XTC files (apparently due to hardware problems or NFS errors). Rescuing them made me (up to now) just loose about 10 frames in 2500, so I think this is still acceptable and avoids re-running the simulations. Uploaded 23:02 August 16, 2004 by Marc Baaden (baaden at smplinux.de)

Oliver Beckstein added Large File Support to this program. This is a utility to rescue partly corrupted XTC files. It works under Linux and is based on earlier files contributed for SGI (see README.rescue) The actual files are called gmx_rescue.c and README.rescue. It came in handy for me because a lot of simulations that I had run on some supercomputer had corrupted XTC files (apparently due to hardware problems or NFS errors). Rescuing them made me (up to now) just loose about 10 frames in 2500, so I think this is still acceptable and avoids re-running the simulations. Uploaded 12:16 September 12, 2004 by Marc Baaden (baaden at smplinux.de)

nr2nametop replaces the atom numbers in your topology with atom name labels. renumtop renumbers all atom numbers (or replaces labels by numbers) in your topology. nr2nametop can be used to convert an .itp file into an .rtp entry. renumtop can be used to manually add or remove atoms from a topology and even to merge two topologies. Using nr2nametop can be helpful to tweak your molecules parameters because when defining e.g. a bond you see which atoms it connects. renumtop will change the labels back to numbers. Finally, process_top writes out a topology with all parameters and atom names explicit, for example to be used as a table in a publication. Uploaded 09:40 July 27, 2004 by Anton Feenstra (feenstra at few.vu.nl)

g_ri3Dc grid-counts atoms or molecules from an index file and writes a 3D density file (portable xdr format). The analysis tool a_ri3Dc reads the 3D density and can convert it into gOpenMols plt format (can be imported into VMD), ascii dump, or it can do 2D slices (in xfarbe format) or cylindrical averages (see these examples), useful for looking at ion channels. See the README and INSTALL for compilation instructions. gricount 1.0 is (1) GPL, (2) can be compiled in the Gromacs source tree or standalone. Uploaded 17:30 March 23, 2004 by Oliver Beckstein (oliver@biop.ox.ac.uk)

This patch against gromacs 3.1.4 includes a tool (make_edi) to generate ED sampling input (.edi) files based on g_covar (or g_nmeig) output. Additionally, the ED sampling module of mdrun has been extended to run in parallel (in the most common cases at least). See the README in the tar file for additional info. Uploaded 13:42 April 02, 2003 by Oliver Lange (olange@gwdg.de)

This is a perl script aimed at simplifying the task of running a Gromacs simulation of a protein, with ions in a box of water molecules. The simulation consists of minimisation, restrained water MD, then fully unrestrained MD. Edit the script to change simulation parameters. to run just use "gromacs_protein_md.pl myfile.pdb". The number of ions is calculated to be a minimal set based upon the number of acidic and basic residues. This script was produced by the chemical informatics team at Syngenta Limited in the UK. It is released under GPL v2.

GUIMACS is a java based front-end program for GROMACS. This is mainly targeted at pure biologists to ease the use of the Groningen Simulation Machine. The current version (version - 1.0) is capable of running automated simulations, given a pdb file containing starting structure of a protein. GUIMACS is distributed under GPL. So, kindly contribute to its development by reporting error and bugs. Please go to GUIMACS homepage for more information on using the program. Homepage: http://pradeepkota.info/projects/guimacs

Hamiltonian REMD code, modified md.c file, external energy calculation script and a short introduction.

A modified version of mdrun that can be used to make a hole in a lipid bilayer that is the right shape to drop in the membrane protein of your choice. It does this by reading a molecular surface file made by Grasp or MSMS. It can also make a cylindrical hole. Tar file contains documentation. Uploaded 15:19 October 15, 2002 by Graham R. Smith (smithgr@cancer.org.uk)

contains fixes to rotamer multiplicities, transitions, occupancies, order params; allows the calculation of a \"cumulative rotamer\" for a whole sidechain Uploaded 20:08 February 12, 2003 by Graham Smith (smithgr@cancer.org.uk)

Python script (and some attached examples) to extract the hydrogen bond existences from HB Map file (.xpm) generated by h_bond from GROMACS. readHBmap.py outputs a list with donor-acceptor pairs with occupancy above the user-input threshold. The script also outputs a file which describes the occupancy over time, and although it is by default formatted to be read by Grace (xmgrace), it can be plotted with other spreadsheet softwares. If you use this script for your research, please acknowledge it. (Feel free to contact me: rsoares@fcfrp.usp.br, Ricardo O. S. Soares)

Reorder atoms in a topology file. This is intended to replace part of Anton Feenstras topology tools which, due to lack of documentation, I have not been able to make work. Uploaded 21:32 January 16, 2005 by Rudolf Potucek (potucek at ucalgary.ca)

This script replaces a certain number of phospholipids with cholesterol molecules. The cholesterols are rotated around the Z axis with a random angle before inserting into the lipid bilayer. The center of mass of the cholesterol is moved to the center of mass of the original phospholipid.

This is especially useful if you have run some simulations of a system using the -sort -shuffle options of grompp, and some others without the -sort option. You may either want to recover the original order for the resulting files, or convert the initial files to the New Order (TM). Grompp writes an index file that allows you to undo the shuffling, but gives no information on the reordering...

Updated release of StressCPU - we had a new cluster to burn-in! Version 2.0 now supports both ia32 (32bit) as well as x86-64/em64t (64bit) platforms. It is multithreaded (both pthreads and win32 threads) by default and will automatically sense the number of CPUs on Linux, Mac OS X, and windows. It runs slightly hotter, in particular for x86-64 systems, the checks are better, and you can now set it for a fixed excution time, e.g. 12 hours. The package includes pre-compiled binaries for Windows, 32 and 64 bit Linux, and 32 as well as 64 bit OS X.

A modified version of mdrun, incorporating the Temperature-Enhanced Essential dynamics Replica EXchange (TEE-REX) algorithm for GMX 3.3.1 (Biophys J 92:4262-4270 (2007)). Just copy the tar file into your Gromacs source code directory & unpack. Tar file contains documentation.

This is basicly the 4.0 template, with a CUDA kernel added. You could use this to generate faster analysis tools, or to simply experiment with CUDA while using your GROMACS data. As an example, some coordinates are copied to the kernel, then copied back. You will need GROMACS, a CUDA-supported nVidia card and CUDA drivers. Edit the makefile to suit your system. nvcc 3.0 and g++ were used, but other versions/compilers should work.

Builds a Gromacs topology from a Tripos .mol2 file and a force field selected from gaff, amber## (where ## is the two digit year), or Tripos (when available). Uses the files in the antechamber-1.27 dat directories dat/antechamber and dat/leap/parm to build gaff or amber## based topologies. Uses the TAFF* files in the directory pointed to by Tripos variable $TA_ASCTABLES to build Tripos force field based topologies. Has an option for renumbering of atoms and residues to decrease the amount of editing needed to add ligands to a system. Has an option to allow use of measured values for bond lengths and angles. Converts distance restraints in the .mol2 file to Gromacs distance restraints. Has potential expandability to other all atom force fields with addition of appropriate atom type definition files.

topolbuild 1.2.1 Reads a Tripos .mol2 file with charges to generate something approximating gromacs *.gro, *.top, and *.itp files from it based on selected force field parameters. Now supports some united atom force fields. Includes tables to support amber, gaff, glycam, and gmx type force fields. Requires that the *.mol2 file have syntactically correct Tripos atom types and absolutely will not work with other input atom types. Includes capability of pruning dihedral angles to a possibly more reasonable set. Revisions include: 1. Corrected errors in prior version from last minute additions. 2. Corrected output of defines and includes. 3. Refined the gromacs force field tables. 4. Revised log and topology outputs to better reflect the types of dihedrals. 5. Updated parameter files for gaff, glycam, and amber to the versions found in AmberTools 1.2 6. Revised order of setting dihedrals to better reflect tleap or grommp settings. 7. Improved option to prune excess dihedral angles. Most users should be satisfied with the results from setting -purge 1 8. Improper dihedrals generated for amber, glycam, gaff, and Tripos force fields are now included with regular type 1 dihedrals in accordance with the way that amber treats improper dihedrals. 9. Ion type names for the amber force fields now written in the topology as atomic symbol with charge to differentiate from other atom types in some force fields and to match the way they appear in the amber ion types file. Special Processing Used for Gromacs Force Fields Gromacs force fields have a limited set of atom types that are used in multiple chemical environments. This works quite well when one can use a residue types file to generate a topology. This presents problems when the goal is to determine the topology of an arbitrary molecule for which residue type information does not exist. Therefore, conversion to gromacs force fields requires double determination of atom types. A first determination of atom types is performed with a rich set of atom types derived from a combination of the gaff and amber atom type definitions. This assignment is used to determine force constants, bond lengths, angles, dihedral angles, and improper angles. A second determination of atom types is performed to assign the true gromacs atom types to match the atom types in the appropriate ffG####nb.itp from the gromacs distribution. A major problem of this double conversion is that for something found in a residue type file, topolbuild does not always select the exact same parameters as are found in the residue type file’s parameterization. However, tests so far give the same parameterization better than 95% of the time.

Reads a syntactically correct Tripos .mol2 file with charges to generate something approximating gromacs *.gro, *.top, and *.itp files from it based on selected force field parameters. This version adds support for oplsaa. Includes tables to support amber, gaff, glycam, oplsaa, and gmx type force fields.

TopolGen is a Perl script designed to generate an OPLS-AA topology file from an all-atom PDB file. It makes use of the CONECT records in the PDB file to determine all bonded parameters that are written to the .top file. Note that all atoms must be present in the PDB file (yes, even H) and that the atoms must be listed as HETATM entries.

TopolGen has been upgraded to include several new features. Most notable among these are primitive atom type and charge assignment and improvements to the documentation. File I/O is entirely different than version 1.0, so please be sure to read the README file. This version fixes a bug discovered after the initial post of version 1.1 on 10/11/2009.

when doing -fit, allows two index groups to be given: -ns then selects from the structure file and -n selects from the trajectory and controls the output. Output may be slightly different (<= 0.005 A) to the standard version. Uploaded 14:39 December 22, 2002 by Graham Smith (smithgr@cancer.org.uk