Dear Mark: This error is being provoked at the top of the .rtp file when a line with something like "[header]" is not parsing suitably. A while ago I suggested using diff on the .rtp file. Do that.
Would you mind telling me how to do that in detail? I tried the following and it doesn't work. diff [ PDM ] ; designation arbitrary, C1 and C2 is -CH3 [ atoms ] SI1 SI 0.300 1 C1 opls_069 0.000 1 C2 opls_069 0.000 1 O1 opls_108 -0.300 1 [ bonds ] SI1 -O1 SI1 C1 SI1 C2 SI1 O1 O1 +SI1 ; Terminal PDMS residue ("beginning" of chain) ; designation arbitrary, C1 C2 and C3 is -CH3 [ PDMB ] [ atoms ] C1 opls_069 0.000 1 SI1 SI 0.300 1 C2 opls_069 0.000 1 C3 opls_069 0.000 1 O1 opls_108 -0.300 1 [ bonds ] SI1 C1 SI1 C2 SI1 C3 SI1 O1 O1 +SI1 ; Terminal PE residue ("end" of chain) ; designation arbitrary, C1 C2 and C3 is -CH3 [ PDME ] [ atoms ] SI1 SI 0.000 1 C1 opls_069 0.000 1 C2 opls_069 0.000 1 C3 opls_069 0.000 1 [ bonds ] SI1 -O1 SI1 C1 SI1 C2 SI1 C3 diff Thanks a lot in advance! On Mon, May 4, 2009 at 10:15 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > Justin A. Lemkul wrote: >> >> Then it seems clear to me that your installation of Gromacs is faulty. >> Have you tried running the test set (available on the wiki site)? If you >> can describe your computer system (OS, version, compilers used, >> configuration options, etc.) then perhaps someone on the list can spot a >> potential pitfall. >> >> -Justin >> >> Yanmei Song wrote: >>> >>> Dear Justin: >>> >>> Thank you so much for your help earlier. I updated my GROMACS to >>> 4.0.4. When I run pdb2gmx using the following two files. I still got >>> the similar error message: >>> >>> Opening library file ffoplsaa.rtp >>> Opening library file >>> /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat >>> Opening library file >>> /packages/gromacs-4.0.4/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 >>> /packages/gromacs-4.0.4/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 >>> /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat >>> Entries in vdwradii.dat: 28 >>> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat >>> Entries in dgsolv.dat: 7 >>> Opening library file >>> /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat >>> Entries in electroneg.dat: 71 >>> Opening library file >>> /packages/gromacs-4.0.4/share/gromacs/top/elements.dat >>> Entries in elements.dat: 218 >>> Reading pdms2.pdb... >>> Read 13 atoms >>> Opening library file >>> /packages/gromacs-4.0.4/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 3 residues with 13 atoms >>> >>> chain #res #atoms >>> 1 ' ' 3 13 >>> >>> All occupancies are one >>> Opening library file >>> /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp >>> Atomtype 1 >>> Reading residue database... (ffoplsaa) >>> Opening library file ffoplsaa.rtp >>> >>> ------------------------------------------------------- >>> Program pdb2gmx_d, VERSION 4.0.4 >>> Source code file: resall.c, line: 279 >>> >>> Fatal error: >>> in .rtp file at line: >>> >>> >>> ------------------------------------------------------- > > This error is being provoked at the top of the .rtp file when a line with > something like "[header]" is not parsing suitably. A while ago I suggested > using diff on the .rtp file. Do that. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Yanmei Song Department of Chemical Engineering ASU
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php