[gmx-users] Problem with using all hydrogen force field

Sandeep Somani ssomani at bii.a-star.edu.sg
Tue Jan 13 03:37:01 CET 2004

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 used.

We need to use explicit hydrogens for our simulation but are stuck here
.. any pointers ?

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        

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