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> >
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