2015-10-14 13:55 GMT-06:00 Chang Woon Jang <[email protected]>: > Dear Christoph, > > What I mean is that the arguments in the --map-igonore are the molecule > names defined in the xml files <name> </name>. As the molecules get ignored in the mapping, these names are from before the mapping, e.g. the tpr file.
Christoph > > 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. -- 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.
