[gmx-users] Problems with forcefield amber99 in Gromacs

Mark Abraham mark.abraham at anu.edu.au
Sat May 26 03:29:54 CEST 2007

> 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.

As for any molecule you want to have in your topology, you need an
appropriate [ molecule ] section in your .top file, or to #include one
from somewhere else. grompp isn't finding any definition for SOL
compatible with amber99. Look around your .top file, and then in
gromacs/share/top to see where TIP5P might be found. If you don't
understand the #define and #ifdef mechanisms you'll see then google for
how cpp (inside grompp) treats these.

> 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?

IIRC the man page of genbox points out that TIP3P is topologically
identical with SPC, so you can use the spc???.gro file for it.


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