Hello
I have two questions. 

First question:
If you parameterize a force field (which means that you make changes in 
atomtypes.atp, create a new .rtp and a .hdb file, make changes in 
ffnonbonded.itp, create a residuetypes.dat file and finally make symbolic links 
to gromacs) and you use pdb2gmx to get a topology file (topol.top) and this 
file has not all informations or something is wrong what is better: 

1.) Try to fix missing or false information in the topology file (detective 
work in the topology)

or should one

2.) Try to fix something in the created and modified files of the force field 
and parametrization

Second question:
This question is implied in someway: If everything in the parametrization is 
correct will be the topology you get by pdb2gmx alway correct for further 
calculations? 


To summarize: If someone has bad (even false) topology, should you try to fix 
the topology or is a bad topology always a strong identification for bad 
parametrization?

Thanks
Greetings
Lara
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