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

[ssomani]

Hi David 

I tried OPLS but still no luck.

Even tried genion with Na, NA, NA+ (someone earlier in this list
suggested using NA+ for Gromos96), but it continues to give error on
atom/molecule types.

Regards
Sandeep 





On Tue, 2004-01-13 at 16:01, David van der Spoel wrote:
> 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