<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Hello</div><br>I have two questions. <br><br>First question:<br>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: <br><br>1.) Try to fix missing or false information in the topology file (detective work in the topology)<br><br>or should one<br><br>2.) Try to fix something in the created and modified files of the force field and parametrization<br><br>Second question:<br>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? <br><br><br>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?<br><br>Thanks<br>Greetings<br>Lara<br></div></body></html>