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. 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 [EMAIL PROTECTED] ========================================================= _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php