GENRTF: Generates topology from a Protein Data Bank file

Genrtf is a program to convert cartesian coordinates into the CHARMM input files. It provides CHARMM input script with definitions for RTF (CHARMM's Residue Topology File) and template parameters. It also provides PDB (Protein Data Bank format) and CRD (CHARMM's coordinate format), PSF (CHARMM's Protein Structure File) and DCD (binary trajectory file format) files. DCD is for easier use in VMD program. Its usage is primarily for easier transformation of PDB files into CHARMM input script for computer simulations of the biological systems, but it may be used with other systems as well. It also generates enough parameters so that HBUILD (automatic build of coordinates for hydrogens) can be used.

genrtf is included in the www.charmming.org

Input coordinates can be in either XYZ (as produced by MOLDEN), PDB (default) MOL (not MOL2), and CHARMM's CRD format.

If runing ab initio methods with CHARMM, almost no changes are needed for input file, but it can also help to develop parameters for the molecules which are not available in the curent CHARMM version.

genrtf [-p] [-a] [-Q] [-C] [-q ] [-c] [-m] [-x] [-v] file

-p       includes template for parameters
-a       hydrogens (still needs a lot of work)
-Q       add commands to run QM calculation in CHARMM
-C       add commands to run QM with Q-Chem calculation in CHARMM
-c       input file is in CRD format (CHARMM native)
-x       input file is in XYZ format
-m       input file is in MOL format
-P       input file is in simple PDB format
-M       input file is in XYZ format but multiple frames (make movies!)
-19      works with MSI topology/parameters
-v       display the version
-q <int> total charge of the system (QM only)

By default it reads PDB file format

Examples

For example one has optimized molecule from G03, or GAMESS and wants to make some more sophisticated restrain minimizations with the CHARMM program:

1. molden gamess.out
   
2. save as XYZ coordinates in the gamess.xyz file
   
3. genrtf -q 1 -Q -x gamess.xyz
4. In the case you want to develop parameters for this system
   charges are already in the CHARMM input script.

Convert CRD coordinates to PDB format without running CHARMM

• genrtf -c file.crd

Create complete CHARMM input script with all the necessary files to run the molecule. It will add hydrogens to the residues which are specified as HETATM.

• genrtf -a 1hbp.pdb
• at this stage we have too many hydrogens. (The routine
  which adds them needs some work). One can delete them in the
  coordinate file (1hbp.CRD) and rerun genrtf:
• genrtf -c 1hpb.CRD
• charmm < 1hpb.i > 1hpb.out
• at this stage one has hydrogens on all the atoms build by CHARMM

Create high quality movies: Input file is a bunch of frames in XYZ format, the same as for MOLDEN. The output is many .atm files which are used in the movie program. They are converted with the LIGHT program to .ppm, or some other popular format (like .tga) to make movies with the Broadcast2000 for example.

• genrtf -m anim.xyz

Bugs