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<P>Hi all,<BR><BR>I am trying to use the All Hydrogen forcefield (<STRONG>option
1</STRONG> of <EM>pdb2gmx</EM>) for simulation of a
protein. <BR><BR>The protein has a net charge of net charge is -1.
The neutralization is done using <EM>genion</EM> and the .top file is modified
(reduce no of solvent by one; add one Na molecule; add #include "ions.itp" line
in ).<BR><BR>Next for energy minimization grompp is used for generating the .tpr
file but it gives an error: <BR>"Fatal error: atomtype K not
found"<BR><BR>There is no error if Gromacs force field (<STRONG>option
0</STRONG> of <EM>pdb2gmx</EM>) is used.<BR><BR>We need to use explicit
hydrogens for our simulation but are stuck here .. any pointers ?<BR><BR>Thnx in
advance </P>
<P><FONT size=2><FONT size=3>Sandeep</FONT><BR><BR>---<BR>Sandeep
Somani<BR>Research Associate<BR>BioInformatics Institute<BR>Singapore<BR><A
href="http://www.bii.a-star.edu.sg/~ssomani/">http://www.bii.a-star.edu.sg/~ssomani/</A><BR><BR>"Not
everything that counts can be counted, and not everything that can be counted
counts." -- Einstein
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