On Wed, Jan 20, 2021 at 11:40 PM Pragati Sharma <[email protected]> wrote: > > Dear all, > > I have some confusion regarding the molecule name to be put in xml as well as > topology file during IBI. > > In atomistic topology, if the molecule name is 'PI' and for CG, I have taken > 'CGPI'. > > 1. In first map file; in atomistic section; hexane.xml in hexane tutorial, > the names I specified for my molecule are: > > <cg_molecule> > <name>CGPI</name> ; CGPI is the name to be given for CG moleculetype > <ident>PI</ident> ; PI is moleculetype in atomistic topol.top file; In > hexane tutorial, this is 'Protein' This was 'Protein' because the molecule is called like this in topol.top, see: https://github.com/votca/csg-tutorials/blob/master/hexane/atomistic/topol.top#L5 > > 2. In the second mapp file; hexane_cg.xml in 'ibi_all' folder of hexane > tutorial, my names would be > <cg_molecule> > <name>CGPI</name> ; for CG > <ident>PI</ident>; In hexane tutorial, it is 'hexane' , shouldn't it be > 'Protein' like in hexane.xml file. Where does this hexane come from. Is it a > random choice? It depends how you call the molecule in topol.top, it was called hexane in that case: https://github.com/votca/csg-tutorials/blob/master/hexane/ibi_all/topol.top#L13 > <topology> > <cg_beads> > <cg_bead> > <name>A1</name> > <type>A</type> > <mapping>UNITY</mapping> > <beads>1:RES:A1</beads>; In hexane tutorial, instead of 'RES', there > is hex > </cg_bead> > > I have a question here, where does this 'hex' come from. Should I write any > random name here for mapping, like I have written 'RES'. If I put 'PI' or > 'CGPI' here instead of RES. error comes that 1:CGPI:A1, bead is not > recognised.
In the cg case, we called the residue 'hex', hence that showed here, see: https://github.com/votca/csg-tutorials/blob/master/hexane/ibi_all/topol.top#L17 For the mapping will, you can just run "csg_dump --top atomistic_topol.tpr" and look at how the beads are named if you are unsure. Same is true for the molecule identifier, just look at the output of csg_dump to understand what VOTCA reads from the tpr file. Christoph > > 3. In the topol.top file in ibi_all folder. should I write the CG name ( > CGNRP here) in the moleculetype and molecules directive > [moleculetype] > CGNRP 3 > > [ molecules ] > ; Compound #mols > CGNRP 1000 > > A quick help will be very much appreciated. > Thanks > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > 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/CAMpF9Q2-YfSFE41EN4DQF%2Bm1g6nexzmUCtTdjeLGAUvk9Vm0YQ%40mail.gmail.com. -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- 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/CAHG27e7eGLru3er6ALPQuOfjttWFFGC41y_d6DeA-w9we8KBSA%40mail.gmail.com.
