Hi, Michael, 1) add Cu2+ the [atoms], [bonds], etc sections in the .top file. 2) you need to change all the entries in the residue column of the [atoms] section to the same name (e.g. MOL) in both the top file and the gro file, including all the residues of the protein. Gromacs needs to think that it is one big molecule.
Then the distance restraints will work fine. I made a script file in python to change all the entries to the same name. Change the [ molecules ] section to reflect that the protein and the Cu2+ is treated as one molecule. e.g. [ molecules ] ; Compound #mols Protein 1 SOL 88367 Cu2+ 1 to [ molecules ] ; Compound #mols MOL 1 SOL 88367 Good Luck, Art --- "Owen, Michael" <[EMAIL PROTECTED]> wrote: > > Hello, > > I am trying to use NMR restraints to position a Cu2+ > ion around specific residues of a peptide. I added > Cu2+ using "genion" and then initiated "grompp" > before an energy minim minimization. I received the > following error message while executing "grompp": > > > ------------------------------------------------------- > Program grompp, VERSION 3.3.1 > Source code file: toppush.c, line: 1108 > > Fatal error: > [ file "Ab_Cu.top", line 5864 ]: > Atom index (67248) in > distance_restraints out of bounds (1-1) > ------------------------------------------------------- > > > Below is the entry in the topology file. Line 5864 > contains the value 97 and the value 67248 refers is > the atom number of the Cu2+ ion. > > > [ distance_restraints ] > > ;ai aj type index type' low up1 > up2 fac > 67248 97 1 1 1 0.185 > 0.195 0.2 1.0 > 67248 196 1 1 1 0.185 > 0.195 0.2 1.0 > 67248 213 1 1 1 0.185 > 0.195 0.2 1.0 > 67248 148 1 1 1 0.195 > 0.205 0.21 1.0 > > Could you suggest any changes that would eliminate > my error? > > Thanks in advance, > > Michael Owen > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
