[gmx-users] duplicate a molecule

Gabriel Marchand gabriel.marchand at uni-due.de
Thu Nov 20 12:37:17 CET 2008

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
 -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
  -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
-[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
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.

I hope what i ask is clear for you and i would really appreciate your help
or your suggestions.

Best regards.
Gabriel Marchand


PhD student Gabriel Marchand
Universität Duisburg-Essen
Theoretische Chemie    Tel:  ++49 491 577 392 7913
Universitätstr. 5      Fax:  ++49 201 183 2656
45117 Essen            email gabriel.marchand at unidue.de

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