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.
