2015-03-14 14:59 GMT-06:00 Daniel Allen <[email protected]>:
> 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?
First of all make sure to have the latest version of the code as I
fixed the first>0 issue separate from the issue with the wrong atom
types.
I have tested your pdb with the following xml file:
<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>
$ csg_dump --top topol.xml | grep -m 1 -C 1 "molecule: 2"
400 Name 38::H Type H Mass 1 Resnr 37 Resname
molecule: 2 PEO16-PBO22 beads: 401
401 Name 1::H0 Type H0 Mass 1 Resnr 38 Resname
Residue number is correct
$ csg_dump --top topol.xml | grep -m 1 -C 1 WAT
51327 Name 38::H Type H Mass 1 Resnr 4863 Resname
molecule: 129 WAT beads: 1
51328 Name 1::W Type W Mass 1 Resnr 4864 Resname
Types are correct.
Christoph
>
> 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]>:
>> > 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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>> >> >> >> > email to [email protected].
>> >> >> >> > To post to this group, send email to [email protected].
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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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