[gmx-users] (no subject)
spoel at xray.bmc.uu.se
Thu Nov 20 08:25:01 CET 2003
On Wed, 2003-11-19 at 23:42, Jodi Fangman wrote:
> Thank you for your help and the new ions.itp information. I used this new file
> and still recieved the error message No moleculetype K+(or NA+ or Na+) found.
> Do you have any idea why this is still happening? I included the part of my
> topology that I edited to see if there was anything wrong with it.
this looks OK. You were using OPLS weren't you? Don't you get another
error message (earlier) when running grompp ?
Maybe you can send the whole screen output from grompp?
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> ; Include water topology
> #include "ions.itp"
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #include "spc.itp"
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> [ system ]
> ; Name
> UBIQUITIN in 100mM NaCl
> [ molecules ]
> ; Compound #mols
> Protein 1
> SOL 4513
> NA+ 4
> CL- 4
> Thank you
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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