Hi All, when I pdb2gmx on a very small (~20 atoms) peptide, it seemingly got stuck in the middle, showing
==================== Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.rtp Opening library file /share/apps/gromacs407/share/gromacs/top/aminoacids.dat Opening library file /share/apps/gromacs407/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /share/apps/gromacs407/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /share/apps/gromacs407/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /share/apps/gromacs407/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /share/apps/gromacs407/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /share/apps/gromacs407/share/gromacs/top/elements.dat Entries in elements.dat: 218 Opening library file /share/apps/gromacs407/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 14 atoms chain #res #atoms 1 '-' 1 14 No occupancies in AA.gro Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.atp Atomtype 1 ==================== Has anyone come across this before? Thanks, Yao
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