[gmx-users] energy minimization, freeze CA

[Vlad Schepanovsky]

Dear GROMACS users,

Today I want to ask you such a  question:

During the *.PDB file convertion the problem with metalloclusters occured.

Would you be so glad to tell me a Program or INTERNET Server which can make 

the GROMACS topology file from *.PDB coordinate file?

The example is placed below: 

HEADER
HETATM48088  S3A CFN A 496      19.020  30.095  -0.654  1.00 28.14           S  
HETATM48089 FE4  CFN A 496      17.648  31.510   0.444  1.00 18.22          FE  
HETATM48090  S1A CFN A 496      17.596  33.679  -0.182  1.00 20.84           S  
HETATM48091  S4A CFN A 496      17.675  31.515   2.696  1.00 21.80           S  
HETATM48092 FE3  CFN A 496      15.597  31.281   1.867  1.00 20.96          FE  
HETATM48093  S2A CFN A 496      14.687  33.331   1.907  1.00 18.54           S  
HETATM48094 FE7  CFN A 496      14.807  29.375   0.473  1.00 14.46          FE  
HETATM48095  S4B CFN A 496      16.054  27.652  -0.083  1.00 16.72           S  
HETATM48096 MO1  CFN A 496      14.736  28.141  -1.918  1.00 19.20          MO  
HETATM48097  S1B CFN A 496      16.066  29.792  -2.996  1.00 19.45           S  
HETATM48098 FE6  CFN A 496      14.781  30.874  -1.494  1.00 15.92          FE  
HETATM48099 FE2  CFN A 496      15.549  32.776  -0.086  1.00 18.59          FE  
HETATM48100 FE1  CFN A 496      16.920  33.538   2.005  1.00 19.95          FE  
HETATM48101 FE5  CFN A 496      16.857  29.574  -0.929  1.00 19.62          FE  
HETATM48102  S2B CFN A 496      14.224  33.002  -1.884  1.00 23.62           S  
HETATM48103  S3B CFN A 496      13.132  29.510  -0.973  1.00 17.86           S  
HETATM48104  S5A CFN A 496      14.359  29.598   2.628  1.00 15.04           S  
HETATM48105  NX  CFN A 496      15.879  30.892   0.030  1.00 19.82           N  
END

P.S. The PRODRG Server have no deal with Fe-S-Mo, Fe-S-Fe connections.

Your's faithfully,
Vlad Schepanovsky.