[gmx-users] disulphide bonds

rams rams rams.crux at gmail.com
Thu Jun 26 06:11:53 CEST 2008

Dear Gromacs users,

Is there any way to handle the disulphide bond formed between two
independent fragments of a protein ? Precisely it is an inter disulphide
bond between two fragments. If I keep the two fragments as separate objects
while preparing the pdb file (using TER between the two fragments), gromacs
is not asking for the formation of a disulphide bond. If I keep them as a
single object while preparing the input pdb, gromacs could recognize the
disulphide bond but while running the energy minimization its complaining
that the distances are too close.

Is there any way to handle these ? I am also thinking like keep them as
separate objects and imposing positional restraints on both the sulphur
atoms. Is it all right to do that way ?

Please suggest me some thing how to handle these ?

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