[gmx-users] Zn problem

hnam mahnam at ibb.ut.ac.ir
Wed Dec 14 11:36:23 CET 2005

In the name of God 
Hello Gromacs users
I work on adenosine deaminase (ADA). ADA has Zn in its active site and it 
connected to three his and one asp. When I make 
itp file by pdb2gmx , it makes two itp files ,one of them is for protein and 
another is for Zn .
I combined this two itps to one itp file and defined new atom types and new 
his and asp (that are connected to ZN) and also I inserted new parameters in 
ffgmxbon.itp  and ffgmxbn.itp and aminoaside.dat and ffgmx.rtp and ffgmx.atp 
library but when I run grompp it says: fatal error :"no such molecule type 
protein "  and source code file :toppush.c line 1264 .Would you please tell 
me everything that I must do.  
Thank you very much in advance
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University 
P.O.box 1417614411

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