[gmx-users] urea simulation and hdb definition

[Divya Dube]

Dear All,
I am using amber99sb for simulation.

While generating topology file for urea I am getting following error for
hydrogens in urea molecule

gmx pdb2gmx -f sol-d.pdb -o protein1.gro -p topol1.top -ignh -

WARNING: atom H11 is missing in residue URE 1914 in the pdb file
         You might need to add atom H11 to the hydrogen database of
building block URE
         in the file aminoacids.hdb (see the manual)


WARNING: atom H12 is missing in residue URE 1914 in the pdb file
         You might need to add atom H12 to the hydrogen database of
building block URE
         in the file aminoacids.hdb (see the manual)


WARNING: atom H21 is missing in residue URE 1914 in the pdb file
         You might need to add atom H21 to the hydrogen database of
building block URE
         in the file aminoacids.hdb (see the manual)


WARNING: atom H22 is missing in residue URE 1914 in the pdb file
         You might need to add atom H22 to the hydrogen database of
building block URE
         in the file aminoacids.hdb (see the manual)

I have added hydrogens to aminoacids.hdb file for urea in the ff folder as

URE    4
1    3    H11    N1    C    N2
1    3    H12    N1    C    N2
1    3    H21    N2    C    N1
1    3    H22    N2    C    N1

Still the program is not recognizing the hydrogens in urea molecule and
giving the same error.
The urea.itp is given in same amber99sbff folder