[gmx-users] Doubts about rtp, itp and how to modify force fields

Justin Lemkul jalemkul at vt.edu
Fri Sep 15 17:12:05 CEST 2017

On 9/15/17 10:57 AM, Elisa Pieri wrote:
> Dear Gromacs users,
> I'm trying to simulate a system in a membrane. My protein is a rhodopsin
> (which contains the RET chromophore); I already have a forcefield to treat
> the retinal, i.e. a modified version of an Amber94 forcefield.
> Now, I added the membrane in my initial PDB file. I chose Charmm27 to treat
> the POPC (but I am kind of a newbie in the field, should I avoid to mix
> forcefields?). I added the lipids.rtp in the Amber94 forcefield folder,

Yes, you should absolutely avoid mixing force fields.  A force field is a 
self-consistent entity, and without extensive validation, it is not worthwhile 
trying to force incompatible parameter sets to "work together" even if 
syntactically possible within the files.

> changed conveniently the atom names in the PDB file and submitted it to
> pdb2gmx, successfully.
> Then I moved to grompp using the .gro and .top produced, but I get this
> error:
> Fatal error:
> Atomtype NTL not found
> Should I include other files/libraries? Should I completely change the
> approach?
> I am very very new to Gromacs (and I guess that starting by playing with
> force fields is not the best idea ever), but I don't know how to solve
> this. Can you help me? I'm open to change the lipid forcefield, but I
> cannot not use my customized (and till now working) Amber94 forcefield for
> the protein part.

Parametrization of novel species is an advanced topic.  If you have parameters 
from a reliable source, use that force field for everything.  If you decide on a 
different force field (due to better reproduction of important properties or 
whatever reason), you have to come up with or find new parameters that are 
compatible with it.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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