1. Force Fields
  3. Lipids
  5. Martini v.3.0.0 phospholipid itp

normal Martini v.3.0.0 phospholipid itp

  • marcol
  • marcol's Avatar Topic Author
  • Visitor
1 year 2 months ago #9568 by marcol
Martini v.3.0.0 phospholipid itp was created by marcol
Hello. I was trying to simulate a system with a OPPG bilayer, but GROMACS has been returning a fatal error of "No such moleculetype OPPG". My top file has definitely #included the phospholipid itp, and I have checked across all my input files to make sure all nomenclature of OPPG is consistent as "OPPG".

The weird thing is when I took the OPPG section of the martini_v3.0.0_phospholipids_v1.itp out and made a standalone .itp file, replaced the #include statement of the complete phospholipid file with an #include statement of just the standalone OPPG.itp, the GROMACS error is resolved. I suspect there might be some sort of typo (?) in the phospholipid itp file near the OPPG region, but I couldn't locate it.

Thought it might be good to mention it in the forum, but it may also just be my system/me being weird.

Please Log in or Create an account to join the conversation.

More
1 year 2 months ago #9569 by vainikka
Replied by vainikka on topic Martini v.3.0.0 phospholipid itp
Hey.

Thanks for the information. I tried creating a OPPG bilayer and managed to run it by referring a freshly downloaded copy of the "martini_v3.0.0_phospholipids_v1.itp".

If you still have the original, error producing *.top file, could you paste it here?

Please Log in or Create an account to join the conversation.

  • marcol
  • marcol's Avatar Topic Author
  • Visitor
1 year 2 months ago - 1 year 2 months ago #9571 by marcol
Replied by marcol on topic Martini v.3.0.0 phospholipid itp
Hi. I tried 2 different systems, one I built myself, and another using CHARMM-GUI defaults to see if it is something I did wrong. Both gave the same error. I did not edit the itp files.

Here is the .top.
#include "toppar/martini_v3.0.0.itp"
#include "toppar/martini_v3.0.0_ions_v1.itp"
#include "toppar/martini_v3.0.0_nucleobases_v1.itp"
#include "toppar/martini_v3.0.0_phospholipids_v1.itp"
#include "toppar/martini_v3.0.0_phospholipids_v1_matthieu.itp"
#include "toppar/martini_v3.0.0_small_molecules_v1.itp"
#include "toppar/martini_v3.0.0_solvents_v1.itp"
#include "toppar/martini_v3.0.0_sugars_v1.itp"
#include "3nir_proa.itp"

[ system ]
; name
Martini system

[ molecules ]
; name number
PROA 1
OPPG 304
W 11042
NA 431
CL 127
Last edit: 1 year 2 months ago by marcol.

Please Log in or Create an account to join the conversation.

More
1 year 2 months ago #9573 by vainikka
Replied by vainikka on topic Martini v.3.0.0 phospholipid itp
Hi!

Thanks, now the issue starts making a bit more sense.

Turns out that the .itp file distributed by CHARMM-GUI has an error on line 7300.
It reads:
#endif;
It should read:
#endif

You can fix the issue simply by removing the semicolon. I'll see if I can get a hold of the CHARMM-GUI people and notify them.

Please Log in or Create an account to join the conversation.

  • marcol
  • marcol's Avatar Topic Author
  • Visitor
1 year 2 months ago #9574 by marcol
Replied by marcol on topic Martini v.3.0.0 phospholipid itp
Ahh, thank you! I have been mixing and matching the itp files I downloaded from here and from CHARMM-GUI without properly labelling them, as I assumed they would be the same. I should start paying more attention!

Thanks again for your help.

Please Log in or Create an account to join the conversation.

  1. Force Fields
  3. Lipids
  5. Martini v.3.0.0 phospholipid itp
Time to create page: 0.109 seconds