[gmx-users] Problem with using all hydrogen force field
ssomani at bii.a-star.edu.sg
Tue Jan 13 03:37:01 CET 2004
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
"Not everything that counts can be counted, and not everything that can
be counted counts." -- Einstein
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