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

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jan 1 01:46:16 CET 2012

On 1/01/2012 7:45 AM, Lara Bunte wrote:
> 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

If you have done a complete parameterization and constructed a complete 
way for pdb2gmx to built a topology from a coordinate file then the 
problem cannot arise. If you haven't done the former, then go back and 
do it. If you haven't done the latter, then it is probably right to fix 
the contents of the force field directory (rather than the produced 
topology) on the theory that you may want to use the force field again 
some time.

> 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?

They're orthogonal. The topology expresses a particular combination of 
the parameters that implements a model. Both topology and parameters 
have to be right for the model to work, and failure doesn't localize the 
problem to one or the other aspect. Just as with writing, even if the 
parser (grompp) thinks the words you are using make grammatical sense 
(no error, so sufficient parameter values and connectivity), only you 
can judge whether the way in which you have followed the rules should 
make for a meaningful sentence (valid model).

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