[gmx-users] Fatal Error

[David]

On Mon, 2005-10-10 at 14:45 +0530, Amol D. Atre wrote:
> Hello all,
> 
> Trying to generate .gro and .top files from a .pdb file which looks like
> this,
this is not a protein, use prodrg. 
> 
> 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.
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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