2014-10-31 9:57 GMT-06:00 Daniel Allen <[email protected]>: > Sure, topol.xml looks like this: > > <topology base= "B-B.pdb"> > <molecules> > <clear/> > <define name="B" first="1" nbeads="14" nmols="100"/> > </molecules> > </topology> Looks ok to me, can you send topol.xml and B-B.pdb to [email protected] and I will have a further look.
Christoph > > Cheers, Dan. > > > On Friday, 31 October 2014 15:53:05 UTC, Christoph Junghans wrote: >> >> 2014-10-31 5:58 GMT-06:00 Daniel Allen <[email protected]>: >> > Hi Christoph, >> > >> > thanks for your reply. >> > >> > So I installed the 1.3-dev version of votca after your response. >> > However, >> > running the command: >> > >> > $ csg_dump --top topol.xml >> > >> > resulted in the output: >> > "an error occurred: >> > bad lexical cast: source type value could not be interpreted as target" >> > >> > Have you seen this error before, or can you think of anything obvious >> > which >> > might be causing it? >> This is a boost parsing error. Can you post your topol.xml? >> >> > >> > Cheers, Dan. >> > >> > On Monday, 20 October 2014 15:24:31 UTC, Christoph Junghans wrote: >> >> >> >> Hi Dan, >> >> >> >> welcome. >> >> >> >> 2014-10-20 4:37 GMT-06:00 Daniel Allen <[email protected]>: >> >> > Hi there, >> >> > >> >> > I am trying to read in a LAMMPS dump file for a simulation of liquid >> >> > butane >> >> > into csg_stat as a simple example of how to map and process LAMMPS >> >> > trajectories, before moving onto my more complex system of long chain >> >> > polymers. >> >> > >> >> > I know that there are a couple of previous questions regarding LAMMPS >> >> > topologies but I cannot quite get it working. >> >> > >> >> > First I tried using a .pdb file specified in my topol.xml file but >> >> > this >> >> > gave >> >> > an error: >> >> > >> >> > "an error occurred: >> >> > P-P.pdb: unknown topology format" which I find strange because in the >> >> > manual >> >> > it gives an example of using a pdb file for topology, any ideas why >> >> > this >> >> > error would occur? >> >> Which version of VOTCA is that? >> >> In 1.2 the pdb is based on the gromacs reader, which means without >> >> Gromacs you won't be able to use pdb files. >> >> However in 1.3 the pdb reader is independent from the Gromacs library, >> >> so make sure you have the 1.3-dev version installed before going on: >> >> <https://code.google.com/p/votca/wiki/Installing#Development_Version> >> >> Also the lammps dump reader in 1.3 is a bit more versatile. >> >> >> >> > >> >> > Anyway, I then decided to try and use the lammps .dump file as the >> >> > topology >> >> > so topol.xml now looks like this: >> >> > >> >> > <topology base="atoms_nvt_prod.dump">/ITEM >> >> > <molecules> >> >> > <clear/> >> >> > <define name="B" first="1" nbeads="14" nmols="100"/> >> >> > </molecules> >> >> > </topology> >> >> > >> >> > So I have defined one molecule type which consists of 14 atoms and >> >> > there >> >> > are >> >> > 100 molecules in the system beginning at atom 1. >> >> > >> >> > I think the problem lies in the coarse-grained mapping file. When >> >> > listing >> >> > atoms which belong to a particular bead, if the syntax is >> >> > RESID:RESNAME:ATOMNAME then I'm struggling to work out what they >> >> > should >> >> > be >> >> > for my system. >> >> > >> >> > Here is the top of my dump file: >> >> > >> >> > ITEM: TIMESTEP >> >> > 0 >> >> > ITEM: NUMBER OF ATOMS >> >> > 13916 >> >> > ITEM: BOX BOUNDS pp pp pp >> >> > -27.8209 27.7639 >> >> > -27.7926 27.8726 >> >> > -27.6615 27.7715 >> >> > ITEM: ATOMS id type x y z >> >> > 12765 2 -21.1019 -18.5716 -26.1089 >> >> > 12766 1 -21.1227 -18.563 -24.9982 >> >> > 12768 1 -20.1424 -19.0188 -26.4462 >> >> > 9768 1 -25.3608 -20.7513 -21.6347 >> >> > 9766 2 -25.8077 -20.8022 -20.6188 >> >> > 9762 1 -23.0727 -20.4904 -19.9854 >> >> > 9764 1 -25.494 -18.664 -19.9916 >> >> > 9763 2 -25.1286 -19.6941 -19.7923 >> >> > 9767 1 -26.8648 -20.4951 -20.7686 >> >> > 9769 2 -25.9722 -22.1004 -19.9808 >> >> > 9760 1 -23.565 -19.281 -21.2077 >> >> > 9759 2 -23.6425 -19.548 -20.132 >> >> > 13105 2 -25.5908 -19.0274 -24.4098 >> >> > 638 2 -22.4319 -26.8526 -26.9045 >> >> > 9772 1 -26.1693 -22.9545 -20.6634 >> >> > 13106 1 -25.5393 -19.9713 -24.9935 >> >> > 11466 1 -22.2057 -26.6297 -23.7546 >> >> > 11454 1 -26.0494 -24.6427 -23.5225 >> >> > 11458 1 -24.8424 -26.6034 -24.4689 >> >> > 3362 1 -20.4076 -20.3751 -20.0356 >> >> > 639 1 -22.2076 -27.6125 -26.1257 >> >> > >> >> > etc ... >> >> > >> >> > Would RESID just be 1? There is no information about residues in the >> >> > dump >> >> > file, does there need to be? It is possible to printout the molecule >> >> > number >> >> > in the dump file. >> >> > >> >> > For RESNAME, I wouldn't know what to use either. >> >> > >> >> > For ATOMNAME I could use the atom type, so atom name would be "2" for >> >> > C >> >> > and >> >> > "1" for H? >> >> > >> >> > The choice for these labels would be more obvious from my .pdb file: >> >> > >> >> > >> >> > HETATM 1 C7 B A 1 -5.985 7.723 -2.9591.00 0.00 >> >> > C >> >> > HETATM 2 H71 B A 1 -5.479 7.242 -2.1481.00 0.00 >> >> > H >> >> > HETATM 3 H72 B A 1 -5.406 7.617 -3.8531.00 0.00 >> >> > H >> >> > HETATM 4 C8 B A 1 -6.944 7.270 -3.1001.00 0.00 >> >> > C >> >> > HETATM 5 C9 B A 1 -7.523 7.376 -2.2061.00 0.00 >> >> > C >> >> > HETATM 6 H81 B A 1 -6.818 6.231 -3.3221.00 0.00 >> >> > H >> >> > HETATM 7 H82 B A 1 -7.450 7.750 -3.9111.00 0.00 >> >> > H >> >> > HETATM 8 H91 B A 1 -7.017 6.896 -1.3951.00 0.00 >> >> > H >> >> > HETATM 9 C10 B A 1 -8.482 6.923 -2.3471.00 0.00 >> >> > C >> >> > HETATM 10 H92 B A 1 -7.648 8.415 -1.9831.00 0.00 >> >> > H >> >> > HETATM 11 H101 B A 1 -8.357 5.884 -2.5691.00 0.00 >> >> > H >> >> > HETATM 12 H102 B A 1 -8.988 7.404 -3.1581.00 0.00 >> >> > H >> >> > HETATM 13 H73 B A 1 -6.112 8.781 -2.7321.00 0.00 >> >> > H >> >> > HETATM 14 H103 B A 1 -9.071 7.031 -1.4361.00 0.00 >> >> > H >> >> > >> >> > So for the first atom it would be 1:B:C7 for example? >> >> You can simply run >> >> $ csg_dump --top topol.xml >> >> to see how VOTCA see and how it names the beads. >> >> The residue name/number doesn't really matter as long as the triple >> >> "RESID:RESNAME:ATOMNAME" is unique for every bead. >> >> >> >> Cheers, >> >> >> >> Christoph >> >> >> >> > >> >> > >> >> > Any help would be greatly appreciated, >> >> > >> >> > Thanks, Dan. >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > -- >> >> > 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. >> >> > 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 http://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 http://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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
