On Sun, Sep 22, 2019 at 7:48 AM Erez Tamir <[email protected]> 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 > 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: >> >> 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. > 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/c2f225d8-413a-43fb-9fad-fed840fd5a5f%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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