Thank you for your answer. I had tried to change the names before, but the error was then that the atoms were not recognized. Reading your answer made me realize that I had not gone far enough,
The solution I found is to create a residue in the .rtp that has the same features as the terminal AA, but with a different name. Then, the fragment is renamed in the .pdb file according to this new residue (the atoms are renamed to), end the "TER" line is removed. I also added a block in .hdb file. And now it works well ! Thank you again ! Baptiste 2013/3/7 Justin Lemkul <[email protected]> > > > On 3/7/13 5:44 AM, Baptiste Demoulin wrote: > >> Hello Gromacs users, >> >> I try to link a metallic core to its surrounding amino-acids. Everything >> works find for bonding side chains and metal atoms, but I have troubles >> when it comes to bonding COO- group from a terminus ALA. The error printed >> by pdb2gmx is the following : >> >> Program pdb2gmx, VERSION 4.6 >> Source code file: /home1/retegan/software/** >> gromacs-4.6/src/kernel/pgutil.**c, >> line: 126 >> >> Fatal error: >> Residue 334 named ALA of a molecule in the input file was mapped >> to an entry in the topology database, but the atom O used in >> an interaction of type special bond in that entry is not found in the >> input file. Perhaps your atom and/or residue naming needs to be >> fixed. >> >> Here my specbon.dat file : >> >> 22 >> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 >> CYS SG 1 HEM FE 2 0.25 CYS2 HEME >> CYS SG 1 HEM CAB 1 0.18 CYS2 HEME >> CYS SG 1 HEM CAC 1 0.18 CYS2 HEME >> MET SD 1 HEM FE 1 0.24 MET HEME >> CO C 1 HEME FE 1 0.19 CO HEME >> CYM SG 1 CYM SG 1 0.2 CYS2 CYS2 >> HIS NE2 1 FE2 FE 4 0.23 HID FE2 >> HIS NE2 1 OEX MN1 6 0.21 HID OEX >> ASP OD2 1 OEX MN1 6 0.23 ASP OEX >> GLU OE2 1 OEX MN1 6 0.20 GLU OEX >> GLU OE1 1 OEX MN2 6 0.21 GLU OEX >> ASP OD1 1 OEX MN2 6 0.21 ASP OEX >> ALA OXT 1 OEX MN2 6 0.20 ALA OEX >> GLU OE1 1 OEX MN3 6 0.21 GLU OEX >> GLU OE2 1 OEX MN3 6 0.23 GLU OEX >> SOX O 1 OEX MN4 6 0.21 SOX OEX >> ASP OD2 1 OEX MN4 6 0.21 ASP OEX >> GLU OE2 1 OEX MN4 6 0.22 GLU OEX >> SOX O 1 OEX CA1 6 0.25 SOX OEX >> ALA O 1 OEX CA1 6 0.25 ALA OEX >> >> I tried to change the atom names within specbond.dat, in the initial pdb >> file, but nothing has worked yet... Does someone have an idea of what is >> going on ? >> >> > Terminal oxygens are renamed according to the specifications in the > relevant .c.tdb file. A terminal residue has no atom named "O" since the > name is changed. If only one bond is missing, it's probably easiest to > just manually add it to the topology, otherwise remove the offending line > in specbond.dat, see how the terminal oxygens are renamed, and then try > using the relevant atom name(s) for creating your bonds. If that approach > doesn't work, then the only option is manual addition to the topology. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > 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> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
