So, anybody knows why it does that or how to deal with nucleic acids? I only saw one similar question asked recently (with different error) which was also left without answer.
Maiki wrote: > Hi, > > I'm trying to convert protein-DNA complex using pdb2gmx with gromos53a6.ff > > $ pdb2gmx -f del.pdb -o del.gro -p del.top -i del.itp -n del.ndx -ignh > > In gromacs version 4.5-beta2 the result is: > > Processing chain 3 'C' (516 atoms, 25 residues) > There are 0 donors and 0 acceptors > There are 0 hydrogen bonds > Identified residue DT1 as a starting terminus. > Identified residue DA25 as a ending terminus. > 8 out of 8 lines of specbond.dat converted successfully > Warning: 'DT' not found in residue topology database, trying to use 'DTHY' > Start terminus: NH3+ > Warning: 'DA' not found in residue topology database, trying to use 'DADE' > End terminus: COO- > Warning: 'DT' not found in residue topology database, trying to use 'DTHY' > Warning: 'DA' not found in residue topology database, trying to use 'DADE' > Warning: 'DG' not found in residue topology database, trying to use 'DGUA' > (...) > Warning: 'DA' not found in residue topology database, trying to use 'DADE' > > ------------------------------------------------------- > Program pdb2gmx, VERSION 4.5-beta2 > Source code file: pdb2top.c, line: 922 > > Fatal error: > atom N not found in buiding block 1DT while combining tdb and rtp > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php