[gmx-users] pdb2gmx and itp files
shnek at tiscali.cz
Sat Jul 2 19:54:24 CEST 2005
thanks for help, this solves everything!
> If you don't create a new forcefield, pdb2gmx won't recognize your new
> Creating a new forcefield is a reeeeaaaly boring task because you have
> to change lots of files .rtp .hdb .atp .dat ... so it's easyer to use
> .itp and just "#include my_molecule.itp"
> Let me show you an example for urea using an itp file.
> Inicially you will have :
> urea.pdb from PDB.
> urea.itp this is the one you created.
> just do this
> editconf -f urea.pdb -o urea.gro
> ! it must have all hidrogens ! 'editconf'will not build them'
> ! you can also use PRODRG to produce the .gro and .itp files.
> Create a new (blank) topology file and include these lines.
> ; Include forcefield parameters
> #include 'ffG43a1.itp' ;or other forcefield
> #include 'urea.itp' ;the topology you created
> ; Include water topology
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #include "spc.itp"
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> [ system ]
> ; Name
> [ molecules ]
> ; Compound #mols
> UREA 1
_ at _"
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