IBI on polymer chains mixture

[Erez Tamir]

Dear all,

I'm trying to perform IBI on polymer system contains 20 different molecules (each molecule is a polymer chain).

The molecules differ by their structure, but they share the same bond and angle types.

I made different mapping file for each molecule, so in total I have 20 mapping files.

I'm trying to divide each polymer chain to 30 coarse-grained beads.

I'm ussing LAMMPS dump files for trajectory.

When I perform IBI in order to get bonded potentials, this error message appears:

csg_get_interaction_property: cg_bonded name 'bond1-2' appears twice in file(s) ... (list of all my 20 mapping files)

'bond1-2' represents bond between bead type 1 and bead type 2.

My settings file is attached together with one mapping file for example.

I have seen other discussions about IBI on mixtures and I'm not sure if the problem is my scripts or the votca versions I'm using (both 1.4 and 1.5-dev).

I also tried to combine all my 20 mapping files into single molecule mapping file, but then I face inconsistency with my trajectory file.

Any help to overcome this issue would be appreciated

Erez

[Christoph Junghans]

On Wed, Aug 21, 2019 at 1:48 AM Erez Tamir <erez...@gmail.com> wrote:
>
> Dear all,
>
> I'm trying to perform IBI on polymer system contains 20 different molecules (each molecule is a polymer chain).
> The molecules differ by their structure, but they share the same bond and angle types.

I don't think that is something VOTCA supports, you can have multiple
molecule of the same type with same bonds and angle, but different
molecules types that share the same angle isn't something we had in
mind when writing VOTCA.

Hence you will get the error below as the name "bond1-2" appears in
multiple contexts.

You could comment out this line:
https://github.com/votca/csg/blob/master/share/scripts/inverse/functions_common.sh#L273
in your installation and see if the results look reasonable to you,
but I am not guaranteeing anything.

Also for bonded IBI, usually only a 1:1 mapping is required as the MD
is already done on the CG level, but your the mapping file is an
atomistic to cg one, so I am not 100% sure what your trying to do
here.

Christoph

> I made different mapping file for each molecule, so in total I have 20 mapping files.
> I'm trying to divide each polymer chain to 30 coarse-grained beads.
> I'm ussing LAMMPS dump files for trajectory.
> When I perform IBI in order to get bonded potentials, this error message appears:
>
> csg_get_interaction_property: cg_bonded name 'bond1-2' appears twice in file(s) ... (list of all my 20 mapping files)
>
> 'bond1-2' represents bond between bead type 1 and bead type 2.
> My settings file is attached together with one mapping file for example.
>
> I have seen other discussions about IBI on mixtures and I'm not sure if the problem is my scripts or the votca versions I'm using (both 1.4 and 1.5-dev).
>
> I also tried to combine all my 20 mapping files into single molecule mapping file, but then I face inconsistency with my trajectory file.
>
> Any help to overcome this issue would be appreciated
>
> Erez
>

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--
Christoph Junghans
Web: http://www.compphys.de

[Erez Tamir]

Hi,

I overcome the previous issue, and now facing another problem:

After installing the latest stable release v1.5 I have problem reading pdb files that worked fine with older version.

When performing csg_dump or cag_stat for example this error message appears: 

an error occurred:

Misformated pdb file in atom line # 0

 the correct pdb file format requires 80 characters in width. Furthermore,

 to read the topology in from a .pdb file the following attributes must be

 specified:

 Atom Name, Residue Name, Residue Number, x, y, z, charge (optional)

What could be the problem?

Thanks,

Erez

בתאריך יום רביעי, 21 באוגוסט 2019 בשעה 18:23:04 UTC+3, מאת Christoph Junghans:

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[Christoph Junghans]

On Fri, Sep 20, 2019 at 6:21 AM Erez Tamir <erez...@gmail.com> wrote:
>
> Hi,
> I overcome the previous issue, and now facing another problem:
> After installing the latest stable release v1.5 I have problem reading pdb files that worked fine with older version.
> When performing csg_dump or cag_stat for example this error message appears:
>
> an error occurred:
> Misformated pdb file in atom line # 0
> the correct pdb file format requires 80 characters in width. Furthermore,
> to read the topology in from a .pdb file the following attributes must be
> specified:
> Atom Name, Residue Name, Residue Number, x, y, z, charge (optional)
>
> What could be the problem?

We implemented a more strict pdf reader, Josh (CC'ed) can tell you
more, but this error mainly means your pdb doesn't conform to pdb
specification.

I opened an issue here: https://github.com/votca/csg/issues/412 to
discuss the details

Christoph

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[Erez Tamir]

I made some modifications in the pdb file in order to stick to the pdb specifications and now the following message appears:

an error occurred:

map::at

What this error means?

Is this means that votca now can read my pdb file but the file contains another error?

 

בתאריך יום שישי, 20 בספטמבר 2019 בשעה 19:18:45 UTC+3, מאת Christoph Junghans:

[Christoph Junghans]

On Sun, Sep 22, 2019 at 3:38 AM Erez Tamir <erez...@gmail.com> wrote:
>
> I made some modifications in the pdb file in order to stick to the pdb specifications and now the following message appears:
>
> an error occurred:
> map::at
>
> What this error means?
> Is this means that votca now can read my pdb file but the file contains another error?

I think we fixed that error in the development version already.

$ csg_dump --top viton4_10_20_pcff_1.data.mapx.new_v8.pdb
an error occurred:
Mass of element c3A not found.

Which basically means we cannot determine the mass of the c3A atom.
See here for available elements:
https://github.com/votca/tools/blob/master/src/libtools/elements.cc#L194

Christoph

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[Erez Tamir]

Hi Christoph,

 Thank you for answering, your support is invaluable.

I see you get a different error message for the csg_dump command.

I still get the error:

an error occurred:

map::at

Why is this difference? I've installed the latest stable votca version..

I've also tried to find the code file containing this error message and I couldn't find it...

Regarding the atoms' masses: c3A is only the name of the atom for mapping, not the element name.

The corresponding element symbol is defined in the 78th column of the pdb file, isn't votca read this column to define the atom's mass?

 I've looked over the link you  send and the elements symbols in me pdb (C, F, H) appear there.

I'm not sure what should I fix in my files.

בתאריך יום ראשון, 22 בספטמבר 2019 בשעה 15:55:38 UTC+3, מאת Christoph Junghans:

[Christoph Junghans]

On Sun, Sep 22, 2019 at 7:48 AM Erez Tamir <erez...@gmail.com> wrote:
>
> Hi Christoph,
> Thank you for answering, your support is invaluable.
>
> I see you get a different error message for the csg_dump command.
> I still get the error:
>
> an error occurred:
> map::at
>
> Why is this difference? I've installed the latest stable votca version..
> I've also tried to find the code file containing this error message and I couldn't find it...
>
> Regarding the atoms' masses: c3A is only the name of the atom for mapping, not the element name.
> The corresponding element symbol is defined in the 78th column of the pdb file, isn't votca read this column to define the atom's mass?

Apparently not, so we will need to fix that.

Christoph

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[Erez Tamir]

Is this mean I currently can't use version 1.5 with my pdb files?

Is there option for workaround or disabling the rigorous pdb reader in this version?

Is there former version supporting pressure correction for lammps and relative entropy which are important to my research?

What do you suggest?  

בתאריך יום ראשון, 22 בספטמבר 2019 בשעה 17:14:11 UTC+3, מאת Christoph Junghans:

[Christoph Junghans]

On Sun, Sep 22, 2019 at 8:41 AM Erez Tamir <erez...@gmail.com> wrote:
>
> Is this mean I currently can't use version 1.5 with my pdb files?

Correct. Hopefully we will get around to fixing it soon.

> Is there option for workaround or disabling the rigorous pdb reader in this version?

Unfortunately not.

>
> Is there former version supporting pressure correction for lammps and relative entropy which are important to my research?

All these features have been available for a while now, but as always
there might be other problems with older versions.

> What do you suggest?
You could use a different file type as topology, e.g. a gro, dump or xml file.

Alternatively depending on how good your programming skills are you
could try to fix it yourself, you will need to add the reading of the
element symbol here:
https://github.com/votca/csg/blob/master/src/libcsg/modules/io/pdbreader.cc#L213
once you have a fix, please open a pull request on GitHub, so that we
can include it in the mainline of the code.

Christoph

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[Christoph Junghans]

Erez,

On Sun, Sep 22, 2019 at 10:33 AM Christoph Junghans <jung...@votca.org> wrote:
>
> On Sun, Sep 22, 2019 at 8:41 AM Erez Tamir <erez...@gmail.com> wrote:
> >
> > Is this mean I currently can't use version 1.5 with my pdb files?
> Correct. Hopefully we will get around to fixing it soon.

Can you test this fix: https://github.com/votca/csg/pull/423?

Christoph