Hi Sacha, see the cg hexane <http://code.google.com/p/votca/source/browse/hexane/ibi/topol.top?repo=tutorials> or cg spc/e <http://code.google.com/p/votca/source/browse/spce/ibi/topol.top?repo=tutorials> topology as an example.
Before I execute csg_inverse, I normally do a sanity check by run grompp in the IBI main directory. It should give no error message. Then I execute mdrun, which should fail with an error like "table_CG_CG.xvg not found". The missing table will later be generated by VOTCA, see the gromacs.table option inside interaction block of your xml setting file. Remember that the common table "table.xvg" needs to be generated somehow and added to the filelist by you. Cheers, Christoph 2011/7/4 Sacha Mould <[email protected]>: > > Hi all, > > i would like to know which information i need to store on my .top file > in order to run inverse iterative processes using Gromacs. I've used > csg_gmxtopol command to generate a coarse-grained .top file > (csg_gmxtopol --top topol.xml --cg mapping.xml --out cgtopol.top), but > after starting the iterative process (csg_inverse setting.xml), > Gromacs through me an error: > > Fatal error: > Syntax error - File topol.top, line 7 > Last line read: > '[ atomtypes ]' > Invalid order for directive atomtypes > For more information and tips for troubleshooting, please check the > GROMACS > website at http://www.gromacs.org/Documentation/Errors > > I configured .top file of my system with the same sections showed on > the propane tutorial, but is still giving error the same type of > error. The information that i'm giving are [default] [atomtypes] > [moleculetype] [atoms] [bonds] [angles] and [molecules]. > > I wonder if someone can help me. > > Thanks so much in advance. > > All the best, > > Sacha > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > > -- Dr. Christoph Junghans Votca Core Developer Web: http://www.votca.org -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
