I found my mistake to the issue. I had "name" misspelled in the topol.xml file in 2 places.
However, now I'm having an issue where I cannot define beads with the same "name" "Atom CHL in molecule Protein already exists." What is the best way to name things in topol.xml when you have multiple atoms in the same bead for the atomistic topology when the topology is a *dump file? I can name each atom differently but this makes the mapping more difficult. It seems like for the Gromacs example you don't have to do this and is simpler? Does it do this through residue numbering? Thanks. Josh My topol.xml is <topology name="hexane.nvt.dump"> <molecules> <clear/> <molecule name="Protein" nmols="100" nbeads="20"> <bead name="CHL" type="C" mass="12.0110" q="-0.222"/> <bead name="CHL" type="H1" mass="1.0079" q="0.074"/> <bead name="CHL" type="H2" mass="1.0079" q="0.074"/> <bead name="CHL" type="H3" mass="1.0079" q="0.074"/> <bead name="CH2" type="C" mass="12.0110" q="-0.148"/> <bead name="CH2" type="H1" mass="1.0079" q="0.074"/> <bead name="CH2" type="H2" mass="1.0079" q="0.074"/> <bead name="CH2" type="C" mass="12.0110" q="-0.148"/> <bead name="CH2" type="H1" mass="1.0079" q="0.074"/> <bead name="CH2" type="H2" mass="1.0079" q="0.074"/> <bead name="CH2" type="C" mass="12.0110" q="-0.148"/> <bead name="CH2" type="H1" mass="1.0079" q="0.074"/> <bead name="CH2" type="H2" mass="1.0079" q="0.074"/> <bead name="CH2" type="C" mass="12.0110" q="-0.148"/> <bead name="CH2" type="H1" mass="1.0079" q="0.074"/> <bead name="CH2" type="H2" mass="1.0079" q="0.074"/> <bead name="CHR" type="C" mass="12.0110" q="-0.222"/> <bead name="CHR" type="H1" mass="1.0079" q="0.074"/> <bead name="CHR" type="H2" mass="1.0079" q="0.074"/> <bead name="CHR" type="H3" mass="1.0079" q="0.074"/> </molecule> </molecules> </topology> On Sunday, February 12, 2017 at 1:36:38 AM UTC-5, Joshua Moore wrote: > Hello, > > I am trying to get the csg-map step to work for the hexane example, but > using LAMMPS for the atomistic trajectory. I've successfully gotten it to > work for the SPC/E water example > > I am trying to run with > > csg_stat --top topol.xml --trj hexane.nvt.dump --cg hexane.xml --options > settings.xml > > where hexane.nvt.dump is the LAMMPS Dump file > > The other files, topol.xml, hexane.xml and settings.xml are attached, > which I've tried to adapt from the Gromacs hexane atomistic example. > > I am getting "attribute name not found", which I think means I must have a > naming mismatch in the files, but I'm not able to find it. > > Any advice? > > Thanks. > > Josh > -- 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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
