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?
I would be very grateful for any suggestions on this.
Cheers, Dan.
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