Hi all<br><br>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<br><br>[ DRG ]
<br> [ atoms ]
<br>CAA opls_966 0 1
<br>CAF opls_966 0 1
<br>CAB opls_967 0 2
<br>CAC opls_967 0 2
<br>CAD opls_967 0 2
<br>CAE opls_967 0 2
<br>
<br> [ bonds ]
<br>CAA CAB
<br>CAB CAC
<br>CAC CAD
<br>CAD CAE
<br>CAE CAF
<br>
<br> [ angles ]
<br>CAA CAB CAC
<br>CAB CAC CAD
<br>CAC CAD CAE
<br>CAD CAE CAF
<br>
<br> [ dihedrals ]
<br>CAA CAB CAC CAD
<br>CAB CAC CAD CAE
<br>CAC CAD CAE CAF<br><br>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 (<a href="http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041609.html">http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041609.html</a>) previously i used pdb2gmx for other molecules and it worked fine for the oplsaa force field. any help is highly appreciated.<br>
<br>Opening library file ffoplsaa.rtp<br>Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>Opening library file /usr/local/gromacs/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 /usr/local/gromacs/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 vdwradii.dat<br>Entries in vdwradii.dat: 28<br>Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat<br>Entries in dgsolv.dat: 7<br>
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat<br>Entries in electroneg.dat: 71<br>Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat<br>Entries in elements.dat: 218<br>Reading hexane.pdb...<br>
Read 6 atoms<br>Opening library file /usr/local/gromacs/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 6 atoms<br>
<br> chain #res #atoms<br> 1 ' ' 1 6 <br><br>All occupancies are one<br>Opening library file ffoplsaa.atp<br>Atomtype 1<br>Reading residue database... (ffoplsaa)<br>Opening library file ffoplsaa.rtp<br>
<br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 4.0.7<br>Source code file: resall.c, line: 279<br><br>Fatal error:<br>in .rtp file at line:<br><br><br>-------------------------------------------------------<br>
<br>Regards<br>Vinoth<br><br>