Sure, topol.xml looks like this:
<topology base= "B-B.pdb">
<molecules>
<clear/>
<define name="B" first="1" nbeads="14" nmols="100"/>
</molecules>
</topology>
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] <javascript:>>:
>
> > 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.
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > --
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> >>
> >>
> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >
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>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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