[gmx-users] topolbuild 1.1, update to an all-atoms model gromacs topology generator

Bruce Ray brucedray at yahoo.com
Wed Apr 2 22:44:41 CEST 2008

I've made a number of changes to topolbuild to correct
problems, and improve the results.  Version 1.1 is now
available in the user contributions at the gromacs web
site.  The following revisions are included:

 1. Scaled Tripos out of plane bending parameter to
    derive better improper dihedral force field
 2. Corrected an error in nitrogen bond type
    differentiation method.
 3. Corrected error in aromatic bond type
 4. Changed how charge deviations are corrected.
 5. Added code to correctly add charge attributed to
    lone pairs in a Sybyl generated structure to the
    parent atom.
 6. Changed non-bonded parameters output to make
    output for single atom ions into comments.
 7. Corrected analysis of ring types.
 8. Corrected determination of atom types in cases
    where 0 is the expected number of bound atoms,
    bound hydrogens, or bound electron withdrawing
    groups on the atom to which a hydrogen is bound.
 9. Corrected antechamber tables to make CZ of
    arginine be assigned its correct type of CA
    rather than the default type of CM with the
    amber force fields.
10. Improved charge group number assignment.
11. Added option to produce only the coordinates
    (*.gro) file for those cases where one has several
    coordinate sets ("poses") that use the same
12. Included some of the required Tripos, amber, and
    gaff force field tables with my modifications of
    some of them.

As with the original, the required input is a
syntactically correct mol2 file with Tripos atom
types.  At this time, output is still limited to
topologies with amber, gaff, or Tripos force fields.
All options present in the prior version remain as
before.  The -gro option to produce only the
coordinates (*.gro) file is the only option added.
Because I found it necessary to alter some of the
original atom type definition and parameters files,
I am now including those with the program.

I hope this proves useful.



Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273

You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost.  

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