Thanks for this Christoph, I appreciate it. 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] > <javascript:>>: > > 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] > <javascript:>>: > >> > 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] <javascript:> 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] <javascript:>. > >> > To post to this group, send email to [email protected] > <javascript:>. > >> > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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.
