Dear gmx users,<br><br>I want to calculate intermolecular RDF between N and carbonyl oxygen atoms in a DPPC bilayer. As suggested in some mails in the mailing list i wanted to generate one tpr file for the purpose containing exclusion 49 (as united atom model of DPPC contains 50 atoms). But while generating the tpr file using the following command <br>
<br>grompp -f grompp.mdp -p topol.top -c dppc08.pdb -o rdf.tpr <br><br>the grompp program hangs saying<br><br>checking input for internal consistency...<br>processing topology...<br>Opening library file /export/softexport/gromacs/share/gromacs/top/ffG53a6.itp<br>
Opening library file /export/softexport/gromacs/share/gromacs/top/ffG53a6nb.itp<br>Opening library file /export/softexport/gromacs/share/gromacs/top/ffG53a6bon.itp<br>Opening library file /export/softexport/gromacs/share/gromacs/top/ff_dum.itp<br>
Generated 165 of the 1596 non-bonded parameter combinations<br>Opening library file /export/softexport/gromacs/share/gromacs/top/spc.itp<br><br>Excluding 49 bonded neighbours molecule type 'DPPC'<br><br>and does not proceed further. What is wrong? Can anyone please help?<br clear="all">
<br>-- <br>Prithvi Raj Pandey<br><br>