2017-08-29 8:02 GMT-06:00 <[email protected]>: > 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]. > 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]. 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.
trj_2_molecules.pdb
Description: Protein Databank data
