normal Martini v.3.0.0 phospholipid itp

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1 year 4 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.

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1 year 4 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?

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1 year 4 months ago - 1 year 4 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 4 months ago by marcol.

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1 year 4 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.

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1 year 4 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.

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