WARNING 1 [file ffnonbonded.itp, line 3095]:; MEMBRANE PROTEIN

User discussions
1

GROMACS version: 2022.1
GROMACS modification: No
Here post your question:

Hello and thank you for considering this:):

For the below subsection:

Membrane Protein: KALP15 in DPPC

Step Three: Defining the Unit Cell & Adding Solvent

1. Orient the protein and membrane

I adjusted my forcefield appropriately I believe previously and input the below command:

gmx grompp -f minim.mdp -c dppc128.pdb -p topol_dppc.top -o dppc.tpr

and received the following:
WARNING 1 [file ffnonbonded.itp, line 3095]:
Bondtype LJ-14 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.

Is this pivotal to correct or may I maxwarn this Warning?

Thanks:)
Joel

2

Rule for life with GROMACS: never use -maxwarn. Fix the problem.

Look at what is on 3095 and refer back to the steps articulated in the tutorial. You should never get a warning from the tutorial if you follow the instructions correctly.

3

Hi, thank you for your kind update:).