[gmx-users] duplicate a molecule

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 20 13:52:09 CET 2008

Gabriel Marchand wrote:
> Hello gmx-users,
> my aim is to simulate a big nafion polymer in water system.
> I already succeded in simulating one nafion monomer in water by following
> the classical method (writing a .pdb file, defining residues in .rtp,
> defining .itp and so on).
> Now i'm facing two new difficulties.
> First i would like to know if there is a way to duplicate my monomer to
> form a polymer in the pdb format without using a molecule builder, because
> i want the polymer size to be more than 1000 atoms. The momomer, which
> contains 70 atoms, is already defined by several residues and i want to
> keep this definition because it is very useful (if i want to change the
> size of the monomer backbone for example).
>  I tried -merge option of pdb2gmx but it did not ask me if i want to merge
> consecutive chain and i so the numbers of atoms in .pdb and in the
> conf.gro (resulting of pdb2gmx) were the same. So i don't know if it is
> possible to duplicate my monomer unit to form a polymer. I search on this
> mail list and on internet before posting this message but without
> success. If i could avoid to write a script to do that, that would be
> very helpful
> I also wanted to know if there is a way to duplicate the polymer to have
> several molecules of the polymer. I try this command :
> genbox -ci XXX.gro -nmol 4 -box 3 3 3
> and i received this output message
>                                 :-)  genbox  (-:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>  -cp    protein.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
>                                    xml
>  -cs     spc216.gro  Input, Opt., Lib. Generic structure: gro g96 pdb tpr tpb
>                                    tpa xml
>  -ci       mono.gro  Input, Opt!  Generic structure: gro g96 pdb tpr tpb tpa
>                                    xml
>   -o        out.gro  Output       Generic structure: gro g96 pdb xml
>   -p      topol.top  In/Out, Opt. Topology file
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -[no]X       bool   no      Use dialog box GUI to edit command line options
> -nice        int    19      Set the nicelevel
> -box         vector 3 3 3   box size
> -nmol        int    4       no of extra molecules to insert
> -try         int    10      try inserting -nmol*-try times
> -seed        int    1997    random generator seed
> -vdwd        real   0.105   default vdwaals distance
> -shell       real   0       thickness of optional water layer around solute
> -maxsol      int    0       maximum number of solvent molecules to add if
>                             they fit in the box. If zero (default) this is
>                             ignored
> -[no]vel     bool   no      keep velocities from input solute and solvent
> WARNING: masses will be determined based on residue and atom names,
>          this can deviate from the real mass of the atom type
> Opening library file aminoacids.dat
> Opening library file /home/gmarchand/gromacs/top/atommass.dat
> Opening library file /home/gmarchand/gromacs/top/vdwradii.dat
> Opening library file /home/gmarchand/gromacs/top/dgsolv.dat
> #Entries in atommass.dat: 83 vdwradii.dat: 28 dgsolv.dat: 7
> Reading molecule configuration
> Protein
> Containing 66 atoms in 7 residue
> Initialising van der waals distances...
> Try 0
> -------------------------------------------------------
> Program genbox, VERSION 3.3.3
> Source code file: ../../../../src/tools/gmx_genbox.c, line: 313
> Fatal error:
> more then one residue in insert molecules
> program terminated
> -------------------------------------------------------
> "I Calculate My Birthright" (P.J. Harvey)
> and indeed my molecule has several residues.

Well it doesn't have to have several residues. The residue names and 
numbers are a convenience for pdb2gmx to generate a topology, and for 
grompp to check that a topology will match a conformation. Once you have 
your single polymer structure and topology, you can rename the residues 
in a text editor in both files. Now genbox won't complain. Whether it'll 
produce a useful result is another matter.

editconf is another approach. Duplicate your system periodically, and 
then manipulate it afterwards to achieve a satisfactory starting point 
for MD.


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