Dear Christoph, I fix the files and now the mapping works even for larger system with 20 different molecules. As you can see each molecule contains beads of various types and masses. How do I define the mass of each bead type? Should I add this information to the topolgy file (attached)?
Regards, Erez בתאריך יום שלישי, 29 באוגוסט 2017 בשעה 20:54:37 UTC+3, מאת Christoph Junghans: > 2017-08-29 8:02 GMT-06:00 <[email protected] <javascript:>>: > > Hi Christoph, > > > > I followed the manual instructions and fist created input files for > mapping > > single chain. > > My goal is to map the atomistic chains into 10-beads coarse-grained > chains. > > The atomsitic chains have different structures. > That is pitty, for molecules of the same type, you can just use one > mapping file. > > > The files are attached. > > I run cg_map and it works fine: > > cg_map --top topo_1_molecule.xml --trj trj_1_molecule.pdb --cg > > cg_1st_molecule.xml --out cg_1molecule.pdb > > > > I then tried to add another chain as another molecule, using 2 types of > > topolgy files (v1 and v2 following the 2 examples in section 3.3 in the > > manual respectively), and run: > > cg_map --top topo_2_molecules_v1.xml --trj trj_2_molecule.pdb --cg > > "cg_1st_molecule.xml:cg_2nd_molecule.xml " --out cg_2molecules.pdb > > > > for topology file "topo_2_molecules_v1" i've got this error": > > cannot find <1:SL2:c1> in SL2 > You can use > $ csg_dump --top topo_2_molecules_v1.xml > to look at how VOTCA sees the topology. > > For a quick look at the above output, I saw that the residue name of > the 2nd molecule wasn't read correctly. (and hence the is no 1:SL2:c1 > with SL2 being the residue name) > I guess this because the residue numbering in the pdb is relative to > the molecule, but it should be absolute (fix pdb attached) > > With that change: > $ csg_map --top topo_2_molecules_v1.xml --trj trj_2_molecule.pdb --cg > "cg_1st_molecule.xml;cg_2nd_molecule.xml" --out cg_2molecules.pdb > runs, but fails with "cannot find map c11f14hc6", which basially means > you need to add the "c11f14hc6" to cg_2nd_molecule.xml > > Christoph > > > > for topology file "topo_2_molecules_v2" i've got this error": > > RenameMolecules: num molecules smaller than > > (I guess this error indicates that i defined only 2 molecules while the > trj > > file contains 20( > > > > Any suggetions how to proceed? > > > > Thanks a lot, > > Best regards, > > Erez > > > > > > > > > > בתאריך יום חמישי, 24 באוגוסט 2017 בשעה 20:16:12 UTC+3, מאת Christoph > > Junghans: > >> > >> 2017-08-24 8:40 GMT-06:00 <[email protected]>: > >> > Hello votca users, > >> > > >> > I'm trying to create topology and mapping files for coarse-graining > >> > polymer > >> > system with various molecule types (i.e. chains with variuos length > and > >> > chemical structure). > >> > > >> > I'm using atomistic lammps trajectory or .pdb files as basis. > >> > > >> > Would anyone advise what should be the correct form of topology and > >> > mapping > >> > files for such system? > >> Have a look at the manual: doc.votca.org/manual.pdf, section 3.1 for > >> the mapping and section 3.3 for xml topology file (which will work > >> best with LAMMPS). > >> > >> And I would start with a single repeat unit of the polymer. If the > >> unit isn't too big you can use the stock tool > >> http://stock.cmm.ki.si/smt/ interactively. > >> > >> Christoph > >> > > >> > Regards, > >> > Erez > >> > > >> > -- > >> > 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. > >> > >> > >> > >> -- > >> 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > Visit this group at https://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > 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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
topo_20_molecules_v3.xml
Description: XML document
