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

Elisa Pieri elisa.pieri at univ-amu.fr
Fri Sep 15 17:07:42 CEST 2017

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,
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

Fatal error:
Atomtype NTL not found

Should I include other files/libraries? Should I completely change the
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.

Thank you very much for your time,


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