Dear Joshua, On Sun, Feb 12, 2017 at 9:16 AM, Joshua Moore <[email protected]> wrote:
> 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? > Unfortunately, you cannot use multiple times the same bead name as it is directly used as atom name. In fact, the residue name (known from GROMACS) in your case is "Protein"; So the solution will be to change type= -> name= and for the type= you can use first letter of atom. Currently, there is no way to express the concept of molecule that contains multiple residues and is replicated n times. You can have a look into the manual, section 3.3 where the example of butane with advanced xml topology is shown. Best, Jakub > > 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. > -- 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.
