[gmx-users] quality of a topology and pdb2gmx

[Justin A. Lemkul]

Lara Bunte wrote:
> Hi
> 
> If you have a good parametrization of a molecule and it's pdb file and you
> use pdb2gmx for getting a topology, will the topology alway be finished?
> 

If you're dealing with a new residue that you've introduced into the .rtp file, 
the topology is only as good as the completeness of the .rtp file.

> 
> It is usual to fix something in the topology file after pdb2gmx or are
> necessary additions in the topology a hint for a bad or even wrong
> parametrization in the force field?
> 

Making changes, additions, or deletions to a pdb2gmx-generated topology would be 
unusual.  It's not likely a consequence of bad parameterization, rather bad 
construction of the necessary input files.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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