Hi Christoph, I only start from 0 because VOTCA indexes from 0 doesn't it? If I run csg_dump --top topol.xml I get:
"List of molecules: molecule: 1 PEO16-PBO22 beads: 401 0 Name 1::H0 Type H0 Mass 1 Resnr 0 Resname 1 Name 1::O1 Type O1 Mass 1 Resnr 0 Resname 2 Name 1::C1 Type C1 Mass 1 Resnr 0 Resname 3 Name 1::H1 Type H1 Mass 1 Resnr 0 Resname ..................... " So if I were to specify first=1 then I wouldn't be able to correctly map my molecules because I would miss the first atom. Please correct me if I am wrong. Cheers, Dan. On Tuesday, 10 March 2015 21:08:36 UTC, Christoph Junghans wrote: > > 2015-03-10 4:28 GMT-06:00 Daniel Allen <[email protected] <javascript:>>: > > > 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] <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.
