[gmx-users] pdb2gmx and itp files

[Lubos Vrbka]

thanks for help, this solves everything!

regards,
lubos

 > If you don't create a new forcefield, pdb2gmx won't recognize your new
 > molecule.
 > 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"
 > #else
 > #include "spc.itp"
 > #endif
 >
 > #ifdef POSRES_WATER
 > ; Position restraint for each water oxygen
 > [ position_restraints ]
 > ;  i funct       fcx        fcy        fcz
 >   1    1       1000       1000       1000
 > #endif
 >
 > [ system ]
 > ; Name
 > UREA
 >
 > [ molecules ]
 > ; Compound        #mols
 > UREA             1
 >
 >

-- 
Lubos
_ at _"