[gmx-users] Re: Re: topology using prodrg (Diego Nolasco)
Justin A. Lemkul
jalemkul at vt.edu
Sun Jul 6 12:46:30 CEST 2008
If you chose Gromos96.1 then you are indeed using the 43a1 parameter
set. The fact that you are seeing "Gromos87/Gromacs coordinate file"
means that you can use that .gro file with either the Gromos87
simulation program, or Gromacs.
The output you copied and pasted also only says "The Gromacs topology,"
so this should be some indication that your topology is what you should
expect, based on what you requested. There is no mention of Gromos87 in
the topology line. Furthermore, the initial coordinates are not
dependent on the force field anyway.
h a wrote:
> 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. <http://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 [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,
> Are you sure you used prodrg beta?
> 2008/7/4, h a <y600100 at gmail.com <mailto: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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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