2014-10-31 10:56 GMT-06:00 Christoph Junghans <[email protected]>: > 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. Thanks, I got it.
Your pdb is mis-formated. In a pdb file the atom name is supposed to be column 13-16 (http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#ATOM), but in your file it is 14-17. Removing the space in column 13 using: $ sed -i 's/\(.\{12\}\)./\1/' B-B.pdb fixes that. However, there was also a try and catch block missing in our code, which I have fixed now: https://code.google.com/p/votca/source/detail?r=31117aa998ced63f88ae91dab44146bb93aefbce&repo=csg Christoph > > 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 -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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