[gmx-users] Fatal Error

[Amol D. Atre]

Hello all,

Trying to generate .gro and .top files from a .pdb file which looks like
this,

HEADER    Ammonia
COMPND    /home/amol/Gromacs/Mymol/NH3-H2O/NH3.pdb
AUTHOR    GENERATED BY BABEL 2.0a1
ATOM      1  NL   LYS     1      -0.000  -0.000   0.000  1.00  0.00
ATOM      2  H1   ABU     1      -0.914   0.575   0.000  1.00  0.00
ATOM      3  H2   ABU     1       0.955   0.504   0.000  1.00  0.00
ATOM      4  H3   ABU     1      -0.041  -1.079   0.000  1.00  0.00
CONECT     1    2    3    4
CONECT     2    1
CONECT     3    1
CONECT     4    1
MASTER        0    0    0    0    0    0    0    0    4    0    4    0
END

Command line: pdb2gmx -f NH3.pdb -o NH3.gro -p NH3.top

Fatal error: Atom NL in residue LYSH 1 not found in rtp entry with 13 atoms
             while sorting atoms

How to overcome this problem? Can anybody please help?

Thanking in advance.

Regards,
Amol D. Atre.
Lab No.A002,
Chemical Engineering Department,
Mumbai University Institute of Chemical Technology,
Matunga(E), Mumbai-400019.