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: > > On Sun, Sep 22, 2019 at 3:38 AM Erez Tamir <[email protected] > <javascript:>> 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] <javascript:>. > > 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.
