[gmx-users] methanol simulation
Mark.Abraham at anu.edu.au
Thu Jan 6 12:58:02 CET 2011
On 6/01/2011 10:35 PM, mustafa bilsel wrote:
> Hi all,
> I have the following error in grompp before energy minimization:
> No such moleculetype SOL
> I have used grep to count the methanol molecules and added SOL 291
> comment in .top file to tell the number of methanols.
> What is missing there?
> Note: I have used pdb2gmx -f xxx.pdb , that is, I haven't added
> anything like in water simulation -water tip3p. Should we add
> something to tell the gromacs that it is methanol simulation?
The [ molecules ] section of your .top lists the names you gave to the [
moleculetypes ] and the number of such molecules. Apparently you gave no
moleculetype the name "SOL"...
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