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.
