[gmx-users] methanol simulation

[Mark Abraham]

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"...

Mark