[gmx-users] Problems with forcefield amber99 in Gromacs

Maik Goette mgoette at mpi-bpc.mpg.de
Tue May 29 10:43:33 CEST 2007

Have a look into the tar again...

Maybe ffamber_tip3p.gro is what you are searching for....
And to specify Mark's comment:
You may want to include ffamber_tip3p.itp in your topology file.

A further suggestion:
Don't think, a software can undertake the thinking for you...We all are 
waiting for the Do-whatever-I-mean-tool...


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

bo yang wrote:
> Hi,
> I have a question regarding to using forcefield amber99 in Gromacs.
> I have all the parameter files of amber99.
> I am doing the MD of carbon nanotube with DNA.
> I have changed the .pdb file of the DNA according to the instruction.
> I generated the topology of DNA with identifying -water tip5p.gro.
> The topology file of DNA is also generated successful.
> Pymol is used to visualize the DNA structure.
> Now, I am doing the energy minimization. When I use the grompp command,
> the output is that
> "Fatal error:
> No such moleculetype SOL".
> I am wondering can anybody tell me how to use the tip5p model of water.
> Also, actually, I want to do the simulation with tip3p. But I could not 
> find
> tip3p.gro. I checked back. There was also another person asked the same
> question. But, I don't quite following the answer.
> Do you minding telling me more about the process?
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list