Dear Christoph, What I mean is that the arguments in the --map-igonore are the molecule names defined in the xml files <name> </name>.
For example, if the molecule names defined in FirstMol.xml, SecondMol.xml, ThirdMol.xml are firstmolecule, secondmolecule, thirdmolecule, I can use the following options for ignoring second and third molecules. cag_gmxtopol --top topol.tpr --out FirstMol.top --cg "FirstMol.xml;SecondMol.xml;ThirdMol.xml" --map-ignore "secondmolecule;thirdmolecule" or use widecard (*) to find patterns of molecule names. cag_gmxtopol --top topol.tpr --out FirstMol.top --cg "FirstMol.xml;SecondMol.xml;ThirdMol.xml" --map-ignore "second*;third*" Am I right? Thank you very much. Best regards, Changwoon Jang On Wed, Oct 14, 2015 at 3:45 PM, Christoph Junghans <[email protected]> wrote: > 2015-10-14 13:32 GMT-06:00 CHANG <[email protected]>: > > Dear VOTCA, > > > > I understood the argument for --map-ignore. The argument is defined > in > > <name> </name> in xml files. If I would like to ignore the SecondMol and > > ThirdMol, I use the following command. > > > > cag_gmxtopol --top topol.tpr --out FirstMol.top --cg > > "FirstMol.xml;SecondMol.xml;ThirdMol.xml" --map-ignore > "SecondMol;ThirdMol" > Not quite, --map-ignore ignore allows to give molecule names (or > pattern ending/beginning with "*") separated by ";" to ignore. These > name don't necessarily have to correspond to the name of the mapping > files! > > > > > Thanks. > > > > Best regards, > > Changwoon Jang > > > > > > On Wednesday, October 14, 2015 at 2:57:46 PM UTC-4, CHANG wrote: > >> > >> Dear VOTCA users, > >> > >> I am trying to generate CG topology file using csg_gmxtopol. I have > >> three xml files for three types of molecules. I understand that it > cannot > >> create multiple molecules topologies. Therefore, I need to use > --map-ignore > >> option. I am not sure what the argument for --map-ignore options is. > >> > >> Is this xml file or name defined in each xml files? > >> > >> Can I use a separate run of csg_gmxtopol like? > >> > >> csg_gmxtopol --top topol.tpr --out FirstMol.top --cg FirstMol.xml > >> > >> csg_gmxtopol --top topol.tpr --out SecondMol.top --cg SecondMol.xml > >> > >> csg_gmxtopol --top topol.tpr --out ThirdMol.top --cg ThirdMol.xml > >> > >> The topol.tpr is the atomistic trajectory for all three molecules. > >> > >> Thank you very much for your help. > >> > >> > >> Best regards, > >> Changwoon Jang, > >> > > -- > > 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 post to this group, send email to [email protected]. > > Visit this group at http://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > 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 post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > -- 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 post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
