[gmx-users] detective work before or after creating a topology?

[Lara Bunte]

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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