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

[Justin Lemkul]

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

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

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