# Errors about membrane protein simulation

**URL:** <https://gromacs.bioexcel.eu/t/errors-about-membrane-protein-simulation/3393>\
**Category:** User discussions\
**Created:** [January 3, 2022, 8:52am UTC](https://gromacs.bioexcel.eu/t/errors-about-membrane-protein-simulation/3393 "2022-01-03T08:52:07Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![rainbow](https://avatars.discourse-cdn.com/v4/letter/r/7993a0/32.png) [@rainbow](https://gromacs.bioexcel.eu/u/rainbow)\
**Post date:** [January 3, 2022, 8:52am UTC](https://gromacs.bioexcel.eu/t/errors-about-membrane-protein-simulation/3393/1 "2022-01-03T08:52:07Z")

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GROMACS version:2021.4  
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  
with -maxwarn.

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.

Kind Regards,

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [January 3, 2022, 2:44pm UTC](https://gromacs.bioexcel.eu/t/errors-about-membrane-protein-simulation/3393/2 "2022-01-03T14:44:08Z")

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The tutorial tells you how to deal with all of this. Follow the steps carefully. You should never get any errors or warnings if you’ve done things correctly.