When I run csg_dump with a topol.xml like so:
<topology base= "PEO16-PBO22-FULL.pdb">
<molecules>
<clear/>
<define name="PEO16-PBO22" first="1" nbeads="401" nmols="128"/>
<define name="WAT" first="51329" nbeads="1" nmols="6667"/>
</molecules>
</topology>
It doesn't run: "an error occurred:
There are molecules which have the same name but different number of bead
please check the section manual topology handling in the votca manual"
This is because of the c++ indexing thing, so even though atom 57995 is
there in the pdb, it tries to read one more water bead and cannot. If I
then decrease the number of water beads by 1 from 6667 to 6666 then it runs:
List of molecules:
molecule: 1 PEO16-PBO22 beads: 401
1 Name 1::O1 Type O1 Mass 1 Resnr 0 Resname
2 Name 1::C1 Type C1 Mass 1 Resnr 0 Resname
3 Name 1::H1 Type H1 Mass 1 Resnr 0 Resname
4 Name 1::H2 Type H2 Mass 1 Resnr 0 Resname
5 Name 1::C2 Type C2 Mass 1 Resnr 0 Resname
6 Name 1::H3 Type H3 Mass 1 Resnr 0 Resname
7 Name 1::H4 Type H4 Mass 1 Resnr 0 Resname
8 Name 2::O1 Type O1 Mass 1 Resnr 1 Resname
9 Name 2::C1 Type C1 Mass 1 Resnr 1 Resname
...........................
396 Name 38::C4 Type C4 Mass 1 Resnr 37 Resname
397 Name 38::H7 Type H7 Mass 1 Resnr 37 Resname
398 Name 38::H8 Type H8 Mass 1 Resnr 37 Resname
399 Name 38::O Type O Mass 1 Resnr 37 Resname
400 Name 38::H Type H Mass 1 Resnr 37 Resname
401 Name 39::H0 Type H0 Mass 1 Resnr 38 Resname
molecule: 2 PEO16-PBO22 beads: 401
402 Name 1::O1 Type O1 Mass 1 Resnr 38 Resname
403 Name 1::C1 Type C1 Mass 1 Resnr 38 Resname
404 Name 1::H1 Type H1 Mass 1 Resnr 38 Resname
405 Name 1::H2 Type H2 Mass 1 Resnr 38 Resname
406 Name 1::C2 Type C2 Mass 1 Resnr 38 Resname
The first atom is not listed for molecule 1 and also the first atom of
molecule 2 is included in molecule 1, see the H0 atom is in residue 39 but
the polymers contain only 38 residues.
You said that the other programs use human counting but I get the same
error trying to run csg_stat which is fixed by taking off a water molecule.
What do you suggest?
Cheers, Dan.
On Friday, 13 March 2015 21:07:59 UTC, Christoph Junghans wrote:
>
> 2015-03-13 3:21 GMT-06:00 Daniel Allen <[email protected] <javascript:>>:
>
> > Hi Christoph,
> >
> > I only start from 0 because VOTCA indexes from 0 doesn't it? If I run
> > csg_dump --top topol.xml I get:
> >
> > "List of molecules:
> > molecule: 1 PEO16-PBO22 beads: 401
> > 0 Name 1::H0 Type H0 Mass 1 Resnr 0 Resname
> > 1 Name 1::O1 Type O1 Mass 1 Resnr 0 Resname
> > 2 Name 1::C1 Type C1 Mass 1 Resnr 0 Resname
> > 3 Name 1::H1 Type H1 Mass 1 Resnr 0 Resname
> > .....................
> > "
> >
> > So if I were to specify first=1 then I wouldn't be able to correctly map
> my
> > molecules because I would miss the first atom.
> No, the first number here is the bead id, which starts from 0 (due to
> the way how c++ counts) and remember csg_dump is a more a debug tool.
> However, for input file, we are using the human counting system
> (starting with 1).
>
> Christoph
>
> >
> > Please correct me if I am wrong.
> >
> > Cheers, Dan.
> >
> > On Tuesday, 10 March 2015 21:08:36 UTC, Christoph Junghans wrote:
> >>
> >> 2015-03-10 4:28 GMT-06:00 Daniel Allen <[email protected]>:
> >> > Thanks for this Christoph, I appreciate it.
> >> Actually, I found another issue, first <1 is against the spec
> >> described in the manual.
> >> I fixed that, too and added a warning:
> >>
> >>
> https://code.google.com/p/votca/source/detail?r=17177c3d1dea8e1b831efa5fdb1f6a16541a2774&repo=csg#
>
> >>
> >> Christoph
> >>
> >> >
> >> > Dan.
> >> >
> >> > On Monday, 9 March 2015 23:37:01 UTC, Christoph Junghans wrote:
> >> >>
> >> >> 2015-03-09 11:26 GMT-06:00 Daniel Allen <[email protected]>:
> >> >> > Hi Christoph,
> >> >> >
> >> >> > sorry but I am unable to send the file to that email on my gmail
> so I
> >> >> > have
> >> >> > attached it here, I hope that's okay.
> >> >> I found the bug and fixed it:
> >> >>
> >> >>
> >> >> <
> https://code.google.com/p/votca/source/detail?r=399952ee16077cb44ea742645f7ac3a759900c1a&name=stable&repo=csg#>
>
>
> >> >>
> >> >> Christoph
> >> >> >
> >> >> > Cheers, Dan.
> >> >> >
> >> >> >
> >> >> >
> >> >> > On Monday, 9 March 2015 17:00:59 UTC, Christoph Junghans wrote:
> >> >> >>
> >> >> >> 2015-03-09 9:26 GMT-06:00 Daniel Allen <[email protected]>:
> >> >> >> > Hi Votca users,
> >> >> >> >
> >> >> >> > I am having trouble setting up my mapping for a system with 2
> >> >> >> > different
> >> >> >> > molecule types. I am using a pdb file containing the all of the
> >> >> >> > atoms
> >> >> >> > of
> >> >> >> > my
> >> >> >> > polymer and then also the CG water beads that I will be using
> >> >> >> > (which
> >> >> >> > I
> >> >> >> > have
> >> >> >> > already clustered so there is just a 1:1 mapping for those).
> >> >> >> >
> >> >> >> > My topol.xml file looks like this:
> >> >> >> >
> >> >> >> > <topology base= "PEO16-PBO22-FULL.pdb">
> >> >> >> > <molecules>
> >> >> >> > <clear/>
> >> >> >> > <define name="PEO16-PBO22" first="0" nbeads="401"
> >> >> >> > nmols="128"/>
> >> >> >> > <define name="WAT" first="51328" nbeads="1" nmols="6667"/>
> >> >> >> > </molecules>
> >> >> >> > </topology>
> >> >> >> >
> >> >> >> > I have run csg_dump --top topol.xml
> >> >> >> >
> >> >> >> > to check the mapping. The problem is that for my water beads,
> it
> >> >> >> > seems
> >> >> >> > like
> >> >> >> > votca has reopened the pdb file as the index starts from 0 and
> the
> >> >> >> > atom
> >> >> >> > types are incorrect despite the fact that I say first="51328"
> for
> >> >> >> > the
> >> >> >> > water.
> >> >> >> >
> >> >> >> > Is this the wrong way to declare multiple molecule types using
> a
> >> >> >> > pdb
> >> >> >> > topology?
> >> >> >> It looks ok to me, but without the pdb I cannot say much. Can you
> >> >> >> send
> >> >> >> PEO16-PBO22-FULL.pdb to [email protected] and I will have a look!
> >> >> >>
> >> >> >> Christoph
> >> >> >>
> >> >> >> >
> >> >> >> > I would be very grateful for any suggestions on this.
> >> >> >> >
> >> >> >> > Cheers, Dan.
> >> >> >> >
> >> >> >> > --
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> >> >> >> > For more options, visit https://groups.google.com/d/optout.
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> Christoph Junghans
> >> >> >> Web: http://www.compphys.de
> >> >> >
> >> >> > --
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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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>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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