[gmx-users] Re: Re: topology using prodrg (Diego Nolasco)

[Diego Nolasco]

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 <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:
>
>   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 <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 (
> 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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