[gmx-users] energy minimization, freeze CA

[David van der Spoel]

Vlad Schepanovsky wrote:
> 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?
> 
you're on your own here. check literature for force field and make 
parameters your self.

> 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.
> 
> 
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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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