GROMACS modification: No
Dear gmx users,
I am trying to practice membrane protein simulation by referring to the Justin tutorial.
When pasting the information of the lipid.itp file to the ffnonbonded.itp file,
In [ pairtypes ] of ffnonbonded.itp,
Existing OW OW 1 0.0026173456 2.634129e-06 information and
OW OW 1 3.31400e-04 3.36000e-07 information added from lipid.itp is duplicated.
So, I think the following warning has occurred.
WARNING 1 [file ffnonbonded.itp, line 3127]:
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
old: 0.00261735 2.63413e-06 0.00261735 2.63413e-06
new: OW OW 1 3.31400e-04 3.36000e-07
Can I ignore the above error using maxwarn option? Or, which of the two OW OW should be deleted?
Also, there is the following such information in [ pairtypes ] of lipid.itp.
HW HW 1 0.00000e+00 0.00000e+00
HW LP 1 0.00000e+00 0.00000e+00
HW LOS 1 0.00000e+00 0.00000e+00
HW LP2 1 0.00000e+00 0.00000e+00
HW LP3 1 0.00000e+00 0.00000e+00
HW LC3 1 0.00000e+00 0.00000e+00
HW LC2 1 0.00000e+00 0.00000e+00
In the tutorial, if HW is included in the atom type, it should be deleted. Can I just delete the HW HW line (the first line only)? Or, should I delete all the lines that contain HW in the first column?
When I deleted the first line (HW HW line), it gives “Unknown atomtype HW” error.