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

[David van der Spoel]

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
> used.
> 
> 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
> 
> ---
> Sandeep Somani
> Research Associate
> BioInformatics Institute
> Singapore
> http://www.bii.a-star.edu.sg/~ssomani/
> 
> "Not everything that counts can be counted, and not everything that
> can be counted counts." -- Einstein        
-- 
David.
________________________________________________________________________
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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