[gmx-users] Re: Re: topology using prodrg (Diego Nolasco)
nolasco1980 at gmail.com
Mon Jul 7 17:23:12 CEST 2008
Take a look at John Kerrigan's tutorial?
And as said Justin, "There is no mention of Gromos87 in the topology line".
2008/7/6 h a <y600100 at gmail.com>:
> 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:
> # 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
> 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,
> Are you sure you used prodrg beta?
> 2008/7/4, h a <y600100 at gmail.com>:
> > 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 (
> > 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> <
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