Hi all I want to use pdb2gmx to generate hexane topology and hexane.gro file. i have added the atom name in .atp file and corresponding section in .rtp file. i have given below my .rtp entry
[ DRG ] [ atoms ] CAA opls_966 0 1 CAF opls_966 0 1 CAB opls_967 0 2 CAC opls_967 0 2 CAD opls_967 0 2 CAE opls_967 0 2 [ bonds ] CAA CAB CAB CAC CAC CAD CAD CAE CAE CAF [ angles ] CAA CAB CAC CAB CAC CAD CAC CAD CAE CAD CAE CAF [ dihedrals ] CAA CAB CAC CAD CAB CAC CAD CAE CAC CAD CAE CAF but i get the error message as given below and it doesn't generate any .top and .gro file . I searched the mailing list and found a similar post but there is no solution ( http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041609.html) previously i used pdb2gmx for other molecules and it worked fine for the oplsaa force field. any help is highly appreciated. Opening library file ffoplsaa.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Opening library file /usr/local/gromacs/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 /usr/local/gromacs/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 vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading hexane.pdb... Read 6 atoms Opening library file /usr/local/gromacs/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 6 atoms chain #res #atoms 1 ' ' 1 6 All occupancies are one Opening library file ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp ------------------------------------------------------- Program pdb2gmx, VERSION 4.0.7 Source code file: resall.c, line: 279 Fatal error: in .rtp file at line: ------------------------------------------------------- Regards Vinoth
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