[gmx-users] Problems with forcefield amber99 in Gromacs

David van der Spoel spoel at xray.bmc.uu.se
Sat May 26 09:37:29 CEST 2007

Mark Abraham 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.
> 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.
you don't want to use tip5p with amber anyway as it was parameterised to 
work with the amber tip3p variant.

>> 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.
> Mark
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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