[gmx-users] Problem with using all hydrogen force field
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jan 13 09:12:00 CET 2004
On Tue, 2004-01-13 at 03:35, Sandeep Somani wrote:
> Hi all,
> I am trying to use the All Hydrogen forcefield (option 1 of pdb2gmx)
> for simulation of a protein.
> The protein has a net charge of net charge is -1. The neutralization
> is done using genion and the .top file is modified (reduce no of
> solvent by one; add one Na molecule; add #include "ions.itp" line in
> Next for energy minimization grompp is used for generating the .tpr
> file but it gives an error:
> "Fatal error: atomtype K not found"
> There is no error if Gromacs force field (option 0 of pdb2gmx) is
> We need to use explicit hydrogens for our simulation but are stuck
> here .. any pointers ?
your best bet is to move on to OPLS, better all-atom force field and I
think support for K is in the files in 3.1.4
> Thnx in advance
> Sandeep Somani
> Research Associate
> BioInformatics Institute
> "Not everything that counts can be counted, and not everything that
> can be counted counts." -- Einstein
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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