Re: [votca] Mapping and topology files for systems with variuos molecule types

[ereztamir]

Hi Christoph,

I followed the manual instructions and fist created input files for mapping 
single chain.
My goal is to map the atomistic chains into 10-beads coarse-grained chains.
The atomsitic chains have different structures.
The files are attached.
I run cg_map and it works fine:
cg_map --top topo_1_molecule.xml --trj trj_1_molecule.pdb --cg 
cg_1st_molecule.xml --out cg_1molecule.pdb

I then tried to add another chain as another molecule, using 2 types of 
topolgy files (v1 and v2 following the 2 examples in section 3.3 in the 
manual respectively), and run:
cg_map --top topo_2_molecules_v1.xml --trj trj_2_molecule.pdb --cg 
"cg_1st_molecule.xml:cg_2nd_molecule.xml " --out cg_2molecules.pdb

for topology file "topo_2_molecules_v1" i've got this error":
cannot find <1:SL2:c1> in SL2

for topology file "topo_2_molecules_v2" i've got this error":
RenameMolecules: num molecules smaller than
(I guess this error indicates that i defined only 2 molecules while the trj 
file contains 20(

Any suggetions how to proceed?

Thanks a lot,
Best regards,
Erez 




בתאריך יום חמישי, 24 באוגוסט 2017 בשעה 20:16:12 UTC+3, מאת Christoph 
Junghans:

> 2017-08-24 8:40 GMT-06:00  <erez...@gmail.com <javascript:>>: 
> > Hello votca users, 
> > 
> > I'm trying to create topology and mapping files for coarse-graining 
> polymer 
> > system with various molecule types (i.e. chains with variuos length and 
> > chemical structure). 
> > 
> > I'm using atomistic lammps trajectory or .pdb files as basis. 
> > 
> >  Would anyone advise what should be the correct form of topology and 
> mapping 
> > files for such system? 
> Have a look at the manual: doc.votca.org/manual.pdf, section 3.1 for 
> the mapping and section 3.3 for xml topology file (which will work 
> best with LAMMPS). 
>
> And I would start with a single repeat unit of the polymer. If the 
> unit isn't too big you can use the stock tool 
> http://stock.cmm.ki.si/smt/ interactively. 
>
> Christoph 
> > 
> > Regards, 
> > Erez 
> > 
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>
>
> -- 
> Christoph Junghans 
> Web: http://www.compphys.de 
>

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topo_1_molecule.xml
Description: XML document

trj_1_molecule.pdb
Description: application/vnd.palm

cg_1st_molecule.xml
Description: XML document

topo_2_molecules_v2.xml
Description: XML document

topo_2_molecules_v1.xml
Description: XML document

trj_2_molecules.pdb
Description: application/vnd.palm

cg_2nd_molecule.xml
Description: XML document