[gmx-users] disulphide bonds

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jun 26 16:26:27 CEST 2008

Hi Ram,

Check the option -merge of pdb2gmx.



On Thu, Jun 26, 2008 at 6:11 AM, rams rams <rams.crux at gmail.com> wrote:
> 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 ?
> Ram.
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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