<font size="2">Yea I used the beta version and chose the force field GROMOS96.1. But after I run the server I get this output<br> Output example for the input thf.pdb<br><br>*********************************<br>PRODRG> Starting up PRODRG version AA080107.0543<br>
PRODRG> Parameter set 'pd/gromos96' (fftype=2).<br>PRODRG> PDB mode detected.<br>PRODRG> WARNING: deleted hydrogen(s) from your input.<br>PRODRG> Molecule complexity index: 2.00.<br>PRODRG> 8 hydrogen(s) added.<br>
PRODRG> Using charge groups.<br>PRODRG> Net charge on molecule: 0.000<br>PRODRG> 9 partial charges 0 ambiguous<br>PRODRG> 13 bonds 0 ambiguous<br>PRODRG> 25 bond angles 8 ambiguous<br>
PRODRG> 4 improper dihedrals 0 ambiguous<br>PRODRG> 5 dihedrals 0 ambiguous<br>PRODRG> Writing GROMACS topology.<br>PRODRG> GROMACS topology quality on 0-10 scale: 7.8<br>GENDRG> Best structure was iteration 3211 with 3.20067739<br>
PRODRG> Spawning GROMACS version <a href="http://3.3.3.">3.3.3.</a>..<br>PRODRG> RMSD from GROMOS bond ideality (Angstrom) : 0.003<br>PRODRG> RMSD from GROMOS angle ideality (degrees) : 2.895<br>PRODRG> RMSD from GROMOS plane ideality (degrees) : 5.553<br>
PRODRG> Number of improper improper dihedrals : 0<br>PRODRG> RMSD from starting bonds (Angstrom) : 0.011<br>PRODRG> RMSD from starting angles (degrees) : 0.464<br>PRODRG> RMSD from starting planes (degrees) : 0.000<br>
PRODRG> RMSD from starting coords (Angstrom) : 0.012<br>PRODRG> Writing: SCRTHOWMMPG<br>PRODRG> Normal program end.<br><br> <br><br><br>Click to go to the following output:<br><br> Coordinates<br># PDB (all H's [D][V], polar/aromatic H's [D][V], polar H's only [D][V] or no H's [D][V])<br>
# MDL Molfile (all H's [D][V], polar H's only [D][V] or no H's [D][V])<br># GROMOS87/GROMACS (all H's [D], polar/aromatic H's [D] or polar H's only [D])<br>.<br>.<br>.<br>.<br>.<br><br></font><font size="2"><a name="DRGAPH.GRO"><span class="ttt">The GROMOS87/GROMACS coordinate file (polar/aromatic hydrogens)<br>
.<br>.<br>.<br>.<br>.<br></span></a><a name="DRGFIN.GRO">
<span class="ttt">The GROMOS87/GROMACS coordinate file (all hydrogens)<br>.<br>.<br>.<br></span>
<span class="ttt"></span></a><a name="DRGGMX.ITP">The GROMACS topology<br>.<br>.<br>.<br>.<br>.<br>*********************<br><br></a><a name="DRGAPH.GRO"></a></font><font size="2"><a name="DRGAPH.GRO"></a>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 ?<br>
<br>thank you,<br><br>harshith<br><br>>>>>><br>
Are you sure you used prodrg beta?<br><br><a href="http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta" target="_blank">http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta</a><br><br><br>
2008/7/4, h a <<a href="mailto:y600100@gmail.com">y600100@gmail.com</a>>:<br>
><br>
> Dear users,<br>
><br>
> I am modeling polymer surface. I need topology for polystyrene. I used<br>
> prodrg earlier version and beta version but in both cases I get topology<br>
> for only GROMOS87 force field. Can not I get topology for force filed<br>
><br>
> GROMOS96 ?<br>
><br>
> also can anybody let me know what is .itp file for GOMOS87 force filed ( I<br>
> mean similar to "GROMOS96 -> ffG43a1.itp" )<br>
><br>
> thank you,<br>
><br>
> Sincerely<br>
> -------<br>
> A.Harshith(Y6001)<br>
><br>
> department of Bio Science and Bioengineering,<br>
> IIT Kanpur, India.<br>
> <a href="http://home.iitk.ac.in/%7Eharshith" target="_blank">http://home.iitk.ac.in/~harshith</a> <<a href="http://home.iitk.ac.in/%7Eharshith" target="_blank">http://home.iitk.ac.in/%7Eharshith</a>><br>
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