Erez, On Sun, Sep 22, 2019 at 10:33 AM Christoph Junghans <[email protected]> wrote: > > On Sun, Sep 22, 2019 at 8:41 AM Erez Tamir <[email protected]> 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 > > > 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 > > > > > בתאריך יום ראשון, 22 בספטמבר 2019 בשעה 17:14:11 UTC+3, מאת Christoph > > Junghans: > >> > >> 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. > > 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/66128688-4e13-48de-89d1-5e07d9653258%40googlegroups.com. > > > > -- > Christoph Junghans > Web: http://www.compphys.de -- 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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