Take a look at John Kerrigan's tutorial? http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf
And as said Justin, "There is no mention of Gromos87 in the topology line". Diego. 2008/7/6 h a <[EMAIL PROTECTED]>: > Yea I used the beta version and chose the force field GROMOS96.1. But after > I run the server I get this output > Output example for the input thf.pdb > > ********************************* > PRODRG> Starting up PRODRG version AA080107.0543 > PRODRG> Parameter set 'pd/gromos96' (fftype=2). > PRODRG> PDB mode detected. > PRODRG> WARNING: deleted hydrogen(s) from your input. > PRODRG> Molecule complexity index: 2.00. > PRODRG> 8 hydrogen(s) added. > PRODRG> Using charge groups. > PRODRG> Net charge on molecule: 0.000 > PRODRG> 9 partial charges 0 ambiguous > PRODRG> 13 bonds 0 ambiguous > PRODRG> 25 bond angles 8 ambiguous > PRODRG> 4 improper dihedrals 0 ambiguous > PRODRG> 5 dihedrals 0 ambiguous > PRODRG> Writing GROMACS topology. > PRODRG> GROMACS topology quality on 0-10 scale: 7.8 > GENDRG> Best structure was iteration 3211 with 3.20067739 > PRODRG> Spawning GROMACS version 3.3.3... > PRODRG> RMSD from GROMOS bond ideality (Angstrom) : 0.003 > PRODRG> RMSD from GROMOS angle ideality (degrees) : 2.895 > PRODRG> RMSD from GROMOS plane ideality (degrees) : 5.553 > PRODRG> Number of improper improper dihedrals : 0 > PRODRG> RMSD from starting bonds (Angstrom) : 0.011 > PRODRG> RMSD from starting angles (degrees) : 0.464 > PRODRG> RMSD from starting planes (degrees) : 0.000 > PRODRG> RMSD from starting coords (Angstrom) : 0.012 > PRODRG> Writing: SCRTHOWMMPG > PRODRG> Normal program end. > > > > > Click to go to the following output: > > Coordinates > # PDB (all H's [D][V], polar/aromatic H's [D][V], polar H's only [D][V] or > no H's [D][V]) > # MDL Molfile (all H's [D][V], polar H's only [D][V] or no H's [D][V]) > # GROMOS87/GROMACS (all H's [D], polar/aromatic H's [D] or polar H's only > [D]) > . > . > . > . > . > > The GROMOS87/GROMACS coordinate file (polar/aromatic hydrogens) > . > . > . > . > . > The GROMOS87/GROMACS coordinate file (all hydrogens) > . > . > . > The GROMACS topology > . > . > . > . > . > ********************* > > It says that "parameter set 'pd/gromos96' " (in second line) but output was > gromos87 coordinate files, topology files :( . can anybody explain why did > this happen ? am I missing anything ? > > thank you, > > harshith > > >>>>> > Are you sure you used prodrg beta? > > http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta > > > 2008/7/4, h a <[EMAIL PROTECTED]>: > > > > Dear users, > > > > I am modeling polymer surface. I need topology for polystyrene. I used > > prodrg earlier version and beta version but in both cases I get topology > > for only GROMOS87 force field. Can not I get topology for force filed > > > > GROMOS96 ? > > > > also can anybody let me know what is .itp file for GOMOS87 force filed ( > I > > mean similar to "GROMOS96 -> ffG43a1.itp" ) > > > > thank you, > > > > Sincerely > > ------- > > A.Harshith(Y6001) > > > > department of Bio Science and Bioengineering, > > IIT Kanpur, India. > > http://home.iitk.ac.in/~harshith <http://home.iitk.ac.in/%7Eharshith> < > http://home.iitk.ac.in/%7Eharshith> > > > > _______________________________________________ > 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 >
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