2013/5/30 <[email protected]>: > Whats the name of this software? > > I do not have this variable defined... I just meant the shell command "xmlwf", it comes with expat, which you need for VOTCA anyhow.
> On Wednesday, May 29, 2013 4:26:54 PM UTC+1, Christoph Junghans wrote: >> >> 2013/5/29 <[email protected]>: >> > Dear users, >> > >> > i am using Votca and i wish to create CG structure based on my atomistic >> > protein chain - one bead per residue, all the same type. Residues from 1 >> > to >> > 30 in xml A1 - A30 of type A. In atomistic topology my molecule type is >> > Protein_chain_X >> > >> > I run: >> > >> > csg_map --top em.tpr --trj Proc_ready.gro --cg mapping_1bead.xml --out >> > cg_out.gro >> > >> > in xml with <type>Protein_chain_X<type> >> > >> > <cg_molecule> >> > <name>PRO</name> >> > <ident>Protein_chain_X</ident> >> > <type>Protein_chain_X<type> >> > <topology> >> > <cg_beads> >> > <cg_bead> >> > <name>A1</name> >> > <type>A</type> >> > <symmetry>1</symmetry> >> > <mapping>A</mapping> >> > <beads> 1:MET:N 1:MET:H1 1:MET:H2 1:MET:H3 1:MET:CA 1:MET:HA >> > 1:MET:CB 1:MET:HB1 1:MET:HB2 1:MET:CG 1:MET:HG1 b1:MET:HG2 1:MET:SD >> > 1:MET:CE >> > 1:MET:HE1 1:MET:HE2 1:MET:HE3 1:MET:C 1:MET:O </beads> >> > </cg_bead> >> > ..... >> > etc. >> > >> > >> > mapping_1bead.xml: Parse error at line 692 >> > mismatched tag >> > line 692 >> > >> > Where line 692 is the last line of the script: </cg_molecule> >> > >> > Without <type>Protein_chain_X<type> >> There is a backslash missing in the closing tags - </type>. >> >> Sometimes it helps to run: >> $xmlwf mapping_1bead.xml >> to find formatting errors. >> >> Cheers, >> >> Christoph >> > >> > Error: invaid type: wrong type in >> > cg_molecule.topology.cg_beads.cg_bead.symmetry >> > >> > Would you please advise? >> > >> > Steven >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to [email protected]. >> > To post to this group, send email to [email protected]. >> > Visit this group at http://groups.google.com/group/votca?hl=en. >> > For more options, visit https://groups.google.com/groups/opt_out. >> > >> > >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
