<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Hi All,</div><div><br></div><div>when I pdb2gmx on a very small (~20 atoms) peptide, it seemingly got stuck in the middle, showing <br></div><div><br></div><div>====================</div><div>Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.rtp<br>Opening library file /share/apps/gromacs407/share/gromacs/top/aminoacids.dat<br>Opening library file /share/apps/gromacs407/share/gromacs/top/aminoacids.dat<br>WARNING: masses will be determined based on residue and atom names,<br> this can deviate from the real mass of the atom type<br>Opening library file /share/apps/gromacs407/share/gromacs/top/atommass.dat<br>Entries in atommass.dat: 178<br>WARNING: vdwradii will be determined based on residue and atom
names,<br> this can deviate from the real mass of the atom type<br>Opening library file /share/apps/gromacs407/share/gromacs/top/vdwradii.dat<br>Entries in vdwradii.dat: 28<br>Opening library file /share/apps/gromacs407/share/gromacs/top/dgsolv.dat<br>Entries in dgsolv.dat: 7<br>Opening library file /share/apps/gromacs407/share/gromacs/top/electroneg.dat<br>Entries in electroneg.dat: 71<br>Opening library file /share/apps/gromacs407/share/gromacs/top/elements.dat<br>Entries in elements.dat: 218<br>Opening library file /share/apps/gromacs407/share/gromacs/top/xlateat.dat<br>26 out of 26 lines of xlateat.dat converted succesfully<br>Analyzing pdb file<br>There are 1 chains and 0 blocks of water and 1 residues with 14 atoms<br><br> chain #res #atoms<br> 1 '-' 1 14 <br><br>No occupancies in AA.gro<br>Opening library file
/share/apps/gromacs407/share/gromacs/top/ffoplsaa.atp<br>Atomtype 1<br><br></div><div>====================</div><div><br></div><div>Has anyone come across this before?</div><div><br></div><div><br></div><div>Thanks,</div><div><br></div><div><br></div><div>Yao<br></div></div></body></html>