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

[h a]

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>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080706/1ba90a25/attachment.html>