On Sun, Sep 22, 2019 at 3:38 AM Erez Tamir <[email protected]> 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 > > > בתאריך יום שישי, 20 בספטמבר 2019 בשעה 19:18:45 UTC+3, מאת Christoph Junghans: >> >> On Fri, Sep 20, 2019 at 6:21 AM Erez Tamir <[email protected]> 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 >> >> > >> > Thanks, >> > Erez >> > >> > >> > בתאריך יום רביעי, 21 באוגוסט 2019 בשעה 18:23:04 UTC+3, מאת Christoph >> > Junghans: >> >> >> >> On Wed, Aug 21, 2019 at 1:48 AM Erez Tamir <[email protected]> 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 >> >> > >> >> > -- >> >> > You received this message because you are subscribed to the Google >> >> > Groups "votca" group. >> >> > To unsubscribe from this group and stop receiving emails from it, send >> >> > an email to [email protected]. >> >> > To view this discussion on the web visit >> >> > https://groups.google.com/d/msgid/votca/c3488b63-7f74-4f3b-8c96-86cf11621ee9%40googlegroups.com. >> >> >> >> >> >> >> >> -- >> >> Christoph Junghans >> >> Web: http://www.compphys.de >> > >> > -- >> > You received this message because you are subscribed to the Google Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send an >> > email to [email protected]. >> > To view this discussion on the web visit >> > https://groups.google.com/d/msgid/votca/dceb1677-6369-4ac9-bbae-c52ba39928bf%40googlegroups.com. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/1bbedb9c-263a-418a-8b88-9f88df84d7a3%40googlegroups.com. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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