Hey, The problem is likely that pdb2gmx created the bond. It will have given a long bond warning. You can add a ter statement in the pdb file at the break.
Cheers, Tsjerk On Mar 26, 2012 5:49 AM, "Mark Abraham" <[email protected]> wrote: On 26/03/2012 12:20 PM, Jackson Chief wrote: > > I made a model of a receptor protein, bilayer, and ... You have to treat this gap somehow. Either you have to cap the peptide chains (see pdb2gmx -h), or model in the missing residues using some (non-GROMACS) software. > > When I performed equilibration, the output had the C-terminus of one protein fragment connecte... .gro files have coordinates, never bonds. Since you haven't described how you are treating the gap, and haven't said how you've observed the "creation" of a peptide bond, it's hard to give specific guidance. Mark -- gmx-users mailing list [email protected] http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
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