Warning: atom name in .top and .gro does not match

User discussions
1

GROMACS version: 2024.4
GROMACS modification: No

I’m building a coarse-grain (MARTINI) model of lipid droplet. My process is first build a small part (1/27) of the droplet and then use insert-molecules to make the full droplet.
The problem here is that when I worked on the small part, everything is fine (grompp, mdrun). But then when I solvate and try to grompp the full model, I ran into

atom name 305 in new_cube_water.top and new_cube_water.gro does not match (C1A - C1B)
atom name 305 in new_cube_water.top and new_cube_water.gro does not match (C1A - C1B)

atom name 306 in new_cube_water.top and new_cube_water.gro does not match (D2A - C2B)

atom name 306 in new_cube_water.top and new_cube_water.gro does not match (D2A - C2B)

atom name 307 in new_cube_water.top and new_cube_water.gro does not match (C3A - C3B)

atom name 307 in new_cube_water.top and new_cube_water.gro does not match (C3A - C3B)

(more than 20 non-matching atom names)

WARNING 1 [file new_cube_water.top, line 17]:
  35586 non-matching atom names
  atom names from new_cube_water.top will be used
  atom names from new_cube_water.gro will be ignored

after checking, the atom that started to mismatched is part of the original small droplet (which had no problem when running grompp before), so I have no idea why this mismatch happens now.

The new .gro and .top files had been updated for their new number of molecules. All the .itps are the same.

Here’s the full_droplet.top (small_droplet.top is only different in the number of molecules and no W)

#include "martini_v2.0.itp"
#include "martini_v2.0_POPC_02.itp"
#include "martini_v2.0_LPC_01.itp"
#include "martini_v2.0_CHOL_02.itp"
#include "martini_v2.0_CHYO_02.itp"
#include "martini_v2.0_TOG_01.itp"

[ system ]
full cube

[ molecules ]
POPC	675
LPC		81
CHOL	594
CHYO	1620
TOG		189
W		62450

I tried running the full droplet without water, same problem appeared, so it couldn’t have been because of the water or the solvate step.

Any help will be highly appreciated!

Thanks,
Max

2

Just a guess… are you mixing the lipids?

If the 1/27 of the droplet is

POPC     25
LPC          3
CHOL     22
...

and so on, and you repeat this structure 27 times, then your starting .gro file will have mixed lipid tipes with same types in different positions. Something like

first droplet {POPC LPC …}
second droplet {POPC LPC …}
…
twenty-seventh droplet POPC LPC …}

But in your topology you define POPC 675, so GROMACS expects 675 consecutive POPC molecules, while you have 25 followed by 3 LPC etc. If this is the case, you have to reorder the gro file before solvation with some script (like awk or similar) or rewrite your topology to something like

; droplet 1
POPC  25
LPC    3
CHOL  22
CHYO  60
TOG    7
; droplet 2
POPC  25
LPC    3
CHOL  22
CHYO  60
TOG    7
; ...
;droplet 27
POPC  25
LPC    3
CHOL  22
CHYO  60
TOG    7
; here you will add solvation things
W  .....

I would reorder the gro, personally, will save you a lot of headache in later analysis.

3

Yes, my .gro file is indeed in each droplet format. I’ll try and see if this works.

Thanks!