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.
-Justin
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:
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 <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>:
>
> 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>
>
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
