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 ?
Thanks for any help or advice.
Best,
Jakub Krajniak
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