i tried to protonation of all ionizable residues in protein, but it comes with an error.
Select group to process: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Group 0 ( System) has 2443 elements Group 1 ( Protein) has 2443 elements Group 2 ( Protein-H) has 2443 elements Group 3 ( C-alpha) has 299 elements Group 4 ( Backbone) has 897 elements Group 5 ( MainChain) has 1197 elements Group 6 (MainChain+Cb) has 1482 elements Group 7 ( MainChain+H) has 1197 elements Group 8 ( SideChain) has 1246 elements Group 9 ( SideChain-H) has 1246 elements Select a group: 1 Selected 1: 'Protein' Back Off! I just backed up prt_prot.pdb to ./#prt_prot.pdb.2# Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx2.hdb Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx2.atp Atomtype 1 Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx2-n.tdb Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx2-c.tdb WARNING: atom CD not found in residue 10 while adding atom ------------------------------------------------------- Program protonate_mpi_d, VERSION 4.0.5 Source code file: genhydro.c, line: 304 Fatal error: Atom CD not found in residue ILE10 while adding hydrogens ------------------------------------------------------- -- *Best Regards, * B. Sarath Kumar, M.S (By Research), Centre for Biotechnology, Anna University, Chennai.
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