Daniel Seeliger

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The pmx(pymacs) project now lives here:

more software

Examples for using tCONCOORD:

  • A simple tCONCOORD simulation of a protein (Staphylococcal nuclease)
  • Using position constraints / Generating alternate loop configurations
  • Generating conformational ensembles of ligands/compounds

    A simple tCONCOORD simulation of a protein (Staphylococcal nuclease)

    Download the pdb file 1ey4.pdb
    Remove water:
    $ grep -v HOH 1ey4.pdb > tmp.pdb
    Use gromacs pdb2gmx to add hydrogens and prepare energy minimization
    $ pdb2gmx -f tmp.pdb -o gmx.pdb -ignh -ff oplsaa
    Download .mdp file for energy minimization em.mdp
    Do energy minimization with gromacs
    $ grompp -f em.mdp -c gmx.pdb
    $ mdrun -c em.pdb
    Download tCONCOORD parameter file for normal runs: input.cpf
    Do constraint definition with tdist:
    $ tdist -s em.pdb
    Generate 100 structures with tdisco:
    $ tdisco -n 100

    Using position constraints / Generating alternate loop configurations

    Here we generate a set of alternate loop conformations for a protein structure. Download the minimized structure 1ugu_min.pdb
    We take the residues 49-65 as loop and generate an index file which contains two groups, the loop and the rest.
    $ make_ndx -f 1ugu_min.pdb
    > r 49-65
    ( this is now group 10)
    > !10
    Now we have an index file called index.ndx. Group 10 now containts the loop and group 11 the rest of the protein which should remain untouched.
    Now we run tdist with the loop input file loop.cpf.
    tdist -s 1ugu_min.pdb -pos index.ndx -flex index.ndx -inp loop.cpf
    > now choose group 11 for fixed positions and group 10 for flexible residues
    This will generate a topology with position constraints for group 11 and for group 10 only primary structure constraints will be defined. The command
    tdisco -n 10 -cfreq 2000 -op -nofit
    will generate 10 alternate loop conformations and write each structure to a pdb file.

    Generating conformational ensembles of ligands/compounds

    tCONCOORD can also generate conformational ensembles of small organic molecules. Structural constraints (rotatable bonds/planar groups) are estimated from the input structure and default parameters are used as simulation parameters (VDW radii etc.) To generate such an ensemble, simply switch of all constraint settings in the parameter file as in compound.cpf. To examplify the procedure we generate an ensemble of a compound from the ZINC database (http://zinc.docking.org/). Download the compound ZINC00000018_u.pdb. Make sure that we have unique atom names in the pdb file ("C1"..."Cn" instead of n times "C"). Afterwards you can run tdist using
    $ tdist -s ZINC00000018_u.pdb -inp compound.cpf
    and with
    $ tdisco -n 100 -on ensemble.pdb
    100 structures are generated and written as pdb trajectory file.