2015-03-10 4:28 GMT-06:00 Daniel Allen <[email protected]>: > Thanks for this Christoph, I appreciate it. Actually, I found another issue, first <1 is against the spec described in the manual. I fixed that, too and added a warning: https://code.google.com/p/votca/source/detail?r=17177c3d1dea8e1b831efa5fdb1f6a16541a2774&repo=csg#
Christoph > > Dan. > > On Monday, 9 March 2015 23:37:01 UTC, Christoph Junghans wrote: >> >> 2015-03-09 11:26 GMT-06:00 Daniel Allen <[email protected]>: >> > Hi Christoph, >> > >> > sorry but I am unable to send the file to that email on my gmail so I >> > have >> > attached it here, I hope that's okay. >> I found the bug and fixed it: >> >> <https://code.google.com/p/votca/source/detail?r=399952ee16077cb44ea742645f7ac3a759900c1a&name=stable&repo=csg#> >> >> Christoph >> > >> > Cheers, Dan. >> > >> > >> > >> > On Monday, 9 March 2015 17:00:59 UTC, Christoph Junghans wrote: >> >> >> >> 2015-03-09 9:26 GMT-06:00 Daniel Allen <[email protected]>: >> >> > Hi Votca users, >> >> > >> >> > I am having trouble setting up my mapping for a system with 2 >> >> > different >> >> > molecule types. I am using a pdb file containing the all of the atoms >> >> > of >> >> > my >> >> > polymer and then also the CG water beads that I will be using (which >> >> > I >> >> > have >> >> > already clustered so there is just a 1:1 mapping for those). >> >> > >> >> > My topol.xml file looks like this: >> >> > >> >> > <topology base= "PEO16-PBO22-FULL.pdb"> >> >> > <molecules> >> >> > <clear/> >> >> > <define name="PEO16-PBO22" first="0" nbeads="401" nmols="128"/> >> >> > <define name="WAT" first="51328" nbeads="1" nmols="6667"/> >> >> > </molecules> >> >> > </topology> >> >> > >> >> > I have run csg_dump --top topol.xml >> >> > >> >> > to check the mapping. The problem is that for my water beads, it >> >> > seems >> >> > like >> >> > votca has reopened the pdb file as the index starts from 0 and the >> >> > atom >> >> > types are incorrect despite the fact that I say first="51328" for the >> >> > water. >> >> > >> >> > Is this the wrong way to declare multiple molecule types using a pdb >> >> > topology? >> >> It looks ok to me, but without the pdb I cannot say much. Can you send >> >> PEO16-PBO22-FULL.pdb to [email protected] and I will have a look! >> >> >> >> Christoph >> >> >> >> > >> >> > I would be very grateful for any suggestions on this. >> >> > >> >> > Cheers, Dan. >> >> > >> >> > -- >> >> > 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. >> >> >> >> -- >> 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. -- 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.
