[gmx-users] pdb2gmx response time

[Yao Yao]

Hi All,

when I pdb2gmx on a very small (~20 atoms) peptide, it seemingly got stuck in the middle, showing 


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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


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Has anyone come across this before?


Thanks,


Yao
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