2014/1/14 Jakub Krajniak <[email protected]>: > Dear all, > > I am trying to use votca for creating the cg system but I am stuck right > now. > Why the first item is :DUM:, when I am doing the csg_dump --top topol.xml? > I have the topology defined at the .pdb file with very simple xml > definition: > > <topology base="one_100.pdb"> > <box xx="49.276" yy="49.276" zz="49.276" /> > <molecules> > <clear/> > <define name="UNX" first="1" nbeads="4" nmols="100" /> > </molecules> > </topology> > > and when I run the csg_dump: > > $ csg_dump --top topol.xml > ... > List of molecules: > molecule: 1 UNX beads: 4 > 0 Name 1:DUM:C1 Type C1 Mass 1 > 1 Name 1:DUM:C2 Type C2 Mass 1 > 2 Name 1:DUM:C2 Type C2 Mass 1 > 3 Name 1:DUM:C1 Type C1 Mass 1 > molecule: 2 UNX beads: 4 > 4 Name 1:UNX:C1 Type C1 Mass 1 > 5 Name 1:UNX:C2 Type C2 Mass 1 > 6 Name 1:UNX:C2 Type C2 Mass 1 > 7 Name 1:UNX:C1 Type C1 Mass 1 > ... > > Running the csg_stats on the trajectory (also pdb) file cause such error: > > $ csg_stat --top topol.xml --trj traj.pdb --cg cg.xml --options settings.xml > begin to calculate distribution functions > # of bonded interactions: 0 > # of non-bonded interactions: 3 > WARNING: topology created from .pdb file, charges and masses are wrong! > I have 400 beads in 100 molecules > cannot find: <1:UNX:C1> in UNX > an error occurred: > mapping error: molecule 1:UNX:C1 does not exist > > Right now I defined the beads as follow > <cg_bead> > <name>A1</name> > <type>A</type> > <symmetry>1</symmetry> > <mapping>A1</mapping> > <beads>1:UNX:C1 1:UNX:C2</beads> > </cg_bead> > > and in my pdb file the ATOM definition is: > ATOM 1 C1 UNX F 0 30.126 22.904 25.307 0.00 0.00 T0000 > ATOM 2 C2 UNX F 0 31.186 23.615 26.184 0.00 0.00 T0000 > ... > > What name should I use in the cg.xml file to proper map the all-atom > description with the cg beads A1 ? Everything seems to be right for the VOTCA point of view.
Which version of VOTCA are you using? In VOTCA < 1.3, we use libgmx to read pdbs, so the bug might be in libgmx. (My guess is that the resnr have to >0, in your pdb is starts with 0) In VOTCA >=1.3, we use just a pure c++ pdb reader to allow pdb support without libgmx, which just reads in the string from the pdb. Cheers, Christoph > > Thanks for any help or advice. > > Best, > Jakub Krajniak > > -- > 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/groups/opt_out. -- 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/groups/opt_out.
