I have found out that there was always the same residue number for all the dummy atoms. Perhaps that was the failure. Now I changed it so that they have all different residue numbers. But now I get the error:
Atom N is used in an interaction of type improper in the topology database, but an atom of that name was not found in residue number 309. when I want to put hydrogens to the structure. pdb2gmx -f 3m71_mod.pdb -o 3m71.gro -p 3m71.top -water tip3p -ff amber03 2>>l ogErr 1>>logOut Bests > > > On 6/28/12 10:11 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi everybody, >> I have an protein structure with many dummy atoms around it simulating >> the >> membrane around the protein. Those dummy atoms are signed in the file as >> an ATOM. >> When I want to put this protein with the membrane in a box with the >> command >> >> editconf -f 3m71.gro -o 3m71_box.gro -bt dodecahedron -d 1.0 2>>logErr >> 1>>logOut >> >> >> it removes the membrane dummy atoms except of one Dummy atom. How can >> that >> be. >> What do I have to change? >> > > Does the second line of the .gro file specify the correct amount of atoms? > The > only reason I know of that editconf will truncate the file is if this line > is > incorrect. > > -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 > > ======================================== > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
