GROMACS version: 2020.1-Ubuntu-2020.1-1
GROMACS modification: No
Hi everyone!
My task is to trace the molecular dynamics of berberine in a water box.
Faced the error described in the screenshot below (fatal error).
How can i fix this? Can i get the .tpr file and start energy minimization somehow?
I need help with this question. Thanks!
The error means your topology file is syntactically invalid. Please share the topology file (.top).
“Sorry, new users can not upload attachments.”
Remarks LigParGen generated XPLOR-TOP file for Bonvin group (by Leela Dodda)
set echo=false end
autogenerate angles=True dihedrals=True end
{ atomType mass }
MASS C800 12.0110
MASS C801 12.0110
MASS N802 14.0070
MASS C803 12.0110
MASS C804 12.0110
MASS C805 12.0110
MASS C806 12.0110
MASS C807 12.0110
MASS C808 12.0110
MASS C809 12.0110
MASS C810 12.0110
MASS C811 12.0110
MASS C812 12.0110
MASS C813 12.0110
MASS C814 12.0110
MASS O815 15.9990
MASS C816 12.0110
MASS C817 12.0110
MASS O818 15.9990
MASS C819 12.0110
MASS C820 12.0110
MASS O821 15.9990
MASS O822 15.9990
MASS C823 12.0110
MASS C824 12.0110
MASS H825 1.0080
MASS H826 1.0080
MASS H827 1.0080
MASS H828 1.0080
MASS H829 1.0080
MASS H830 1.0080
MASS H831 1.0080
MASS H832 1.0080
MASS H833 1.0080
MASS H834 1.0080
MASS H835 1.0080
MASS H836 1.0080
MASS H837 1.0080
MASS H838 1.0080
MASS H839 1.0080
MASS H840 1.0080
MASS H841 1.0080
MASS H842 1.0080
MASS H843 1.0080
MASS H844 1.0080
MASS H845 1.0080
MASS H846 1.0080
MASS H847 1.0080
MASS H848 1.0080
MASS H849 1.0080
MASS H850 1.0080
MASS H851 1.0080
MASS H852 1.0080
MASS H853 1.0080
MASS H854 1.0080
MASS H855 1.0080
MASS H856 1.0080
MASS H857 1.0080
RESIdue UNK
GROUP
{ atomName atomType Charge }
ATOM C00 TYPE= C800 CHARGE= 0.063 END
ATOM C01 TYPE= C801 CHARGE= -0.119 END
ATOM N02 TYPE= N802 CHARGE= -0.5364 END
ATOM C03 TYPE= C803 CHARGE= -0.2142 END
ATOM C04 TYPE= C804 CHARGE= -0.1118 END
ATOM C05 TYPE= C805 CHARGE= -0.157 END
ATOM C06 TYPE= C806 CHARGE= 0.0027 END
ATOM C07 TYPE= C807 CHARGE= -0.0424 END
ATOM C08 TYPE= C808 CHARGE= -0.1476 END
ATOM C09 TYPE= C809 CHARGE= -0.1806 END
ATOM C0A TYPE= C810 CHARGE= -0.1712 END
ATOM C0B TYPE= C811 CHARGE= 0.0112 END
ATOM C0C TYPE= C812 CHARGE= -0.1456 END
ATOM C0D TYPE= C813 CHARGE= -0.1721 END
ATOM C0E TYPE= C814 CHARGE= 0.0315 END
ATOM O0F TYPE= O815 CHARGE= -0.3769 END
ATOM C0G TYPE= C816 CHARGE= 0.0757 END
ATOM C0H TYPE= C817 CHARGE= -0.2176 END
ATOM O0I TYPE= O818 CHARGE= -0.3679 END
ATOM C0J TYPE= C819 CHARGE= 0.1554 END
ATOM C0K TYPE= C820 CHARGE= 0.0175 END
ATOM O0M TYPE= O821 CHARGE= -0.376 END
ATOM O0N TYPE= O822 CHARGE= -0.3674 END
ATOM C0O TYPE= C823 CHARGE= -0.094 END
ATOM C0P TYPE= C824 CHARGE= -0.074 END
ATOM H0Q TYPE= H825 CHARGE= 0.0987 END
ATOM H0R TYPE= H826 CHARGE= 0.1201 END
ATOM H0S TYPE= H827 CHARGE= 0.1197 END
ATOM H0T TYPE= H828 CHARGE= 0.1052 END
ATOM H0U TYPE= H829 CHARGE= 0.1052 END
ATOM H0V TYPE= H830 CHARGE= 0.1094 END
ATOM H0W TYPE= H831 CHARGE= 0.1031 END
ATOM H0X TYPE= H832 CHARGE= 0.1031 END
ATOM H0Y TYPE= H833 CHARGE= 0.0981 END
ATOM H0Z TYPE= H834 CHARGE= 0.1018 END
ATOM H10 TYPE= H835 CHARGE= 0.1173 END
ATOM H11 TYPE= H836 CHARGE= 0.1173 END
ATOM H12 TYPE= H837 CHARGE= 0.1033 END
ATOM H13 TYPE= H838 CHARGE= 0.1033 END
ATOM H14 TYPE= H839 CHARGE= 0.1033 END
ATOM H15 TYPE= H840 CHARGE= 0.0863 END
ATOM H16 TYPE= H841 CHARGE= 0.0863 END
ATOM H17 TYPE= H842 CHARGE= 0.0863 END
ATOM H18 TYPE= H843 CHARGE= 0.1196 END
ATOM H19 TYPE= H844 CHARGE= 0.0938 END
ATOM H1A TYPE= H845 CHARGE= 0.0987 END
ATOM H1B TYPE= H846 CHARGE= 0.1066 END
ATOM H1C TYPE= H847 CHARGE= 0.1201 END
ATOM H1D TYPE= H848 CHARGE= 0.1197 END
ATOM H1E TYPE= H849 CHARGE= 0.1356 END
ATOM H1F TYPE= H850 CHARGE= 0.1094 END
ATOM H1G TYPE= H851 CHARGE= 0.0991 END
ATOM H1H TYPE= H852 CHARGE= 0.125 END
ATOM H1I TYPE= H853 CHARGE= 0.0981 END
ATOM H1J TYPE= H854 CHARGE= 0.1087 END
ATOM H1K TYPE= H855 CHARGE= 0.1025 END
ATOM H1M TYPE= H856 CHARGE= 0.1018 END
ATOM H1N TYPE= H857 CHARGE= 0.1085 END
{ Bonds: atomName1 atomName2 }
BOND C01 C00
BOND N02 C00
BOND C03 C00
BOND C04 C01
BOND C05 C01
BOND C06 N02
BOND C07 N02
BOND C08 C03
BOND C09 C04
BOND C0A C04
BOND C0B C05
BOND C0C C06
BOND C0D C08
BOND C0E C09
BOND O0F C0B
BOND C0G C0C
BOND C0H C0D
BOND O0I C0E
BOND C0J O0F
BOND C0K C0G
BOND O0M C0G
BOND O0N C0K
BOND C0O O0M
BOND C0P O0N
BOND H0Q C03
BOND H0R C05
BOND H0S C06
BOND H0T C07
BOND H0U C07
BOND H0V C09
BOND H0W C0A
BOND H0X C0A
BOND H0Y C0D
BOND H0Z C0H
BOND H10 C0J
BOND H11 C0J
BOND H12 C0O
BOND H13 C0O
BOND H14 C0O
BOND H15 C0P
BOND H16 C0P
BOND H17 C0P
BOND H18 C00
BOND H19 C01
BOND H1A C03
BOND H1B C04
BOND H1C C05
BOND H1D C06
BOND H1E C08
BOND H1F C09
BOND H1G C0B
BOND H1H C0C
BOND H1I C0D
BOND H1J C0E
BOND H1K C0G
BOND H1M C0H
BOND H1N C0K
BOND C0A C07
BOND C0C C08
BOND C0E C0B
BOND C0K C0H
BOND C0J O0I
{ Improper Dihedrals: aName1 aName2 aName3 aName4 }
IMPRoper C00 C01 N02 C03
IMPRoper C01 C00 C04 C05
IMPRoper N02 C00 C06 C07
IMPRoper C04 C01 C0A C09
IMPRoper C08 C03 C0C C0D
IMPRoper C0B C05 C0E O0F
IMPRoper C0C C0G C08 C06
IMPRoper C0E C09 O0I C0B
IMPRoper C0G C0K C0C O0M
IMPRoper C0K C0G C0H O0N
IMPRoper C03 C00 H0Q C08
IMPRoper C05 C01 H0R C0B
IMPRoper C06 N02 H0S C0C
IMPRoper C07 N02 H0T C0A
IMPRoper C07 N02 C0A H0U
IMPRoper C09 C04 C0E H0V
IMPRoper C0A C07 C04 H0W
IMPRoper C0A H0X C04 C07
IMPRoper C0D C08 H0Y C0H
IMPRoper C0H H0Z C0K C0D
IMPRoper C0J O0I H10 O0F
IMPRoper C0J O0I H11 O0F
IMPRoper C0O H12 O0M H13
IMPRoper C0O H12 O0M H14
IMPRoper C0P H16 O0N H15
IMPRoper C0P H15 H17 O0N
IMPRoper C00 C01 N02 H18
IMPRoper C01 C00 H19 C04
IMPRoper C03 C00 C08 H1A
IMPRoper C04 C01 H1B C09
IMPRoper C05 C01 C0B H1C
IMPRoper C06 H1D N02 C0C
IMPRoper C08 H1E C03 C0C
IMPRoper C09 H1F C04 C0E
IMPRoper C0B H1G C05 C0E
IMPRoper C0C C08 H1H C06
IMPRoper C0D C08 C0H H1I
IMPRoper C0E C09 C0B H1J
IMPRoper C0G C0K C0C H1K
IMPRoper C0H H1M C0K C0D
IMPRoper C0K C0G H1N C0H
END {RESIdue UNK}
set echo=true end
SOL 221
SOL 392
SOL 414
SOL 414
SOL 414
SOL 396
That is not a GROMACS-formatted topology file.
yeah, im used LigParGen Server to get topology of berberine
is it wrong way?
Aside from the topology not being in the correct format, and as I mentioned before, LigParGen (or any automated parameter assignment method) is almost certainly not going to provide a good model for berberine. I strongly recommend seeing how parameters of other molecules with similar structures (e.g. other dyes that also contain quaternary ammonium groups) have been developed and then do something similar.
Cheers
Tom
I need just to do something like a first step of tutorial for GROMACS " Lysozyme in Water" (Lysozyme in Water), but with Berberine.
Is it really too hard to do?
How can i simplify this task?
Well, it depends on what you’re trying to study and how accurate you want your simulations to be.
Protein and water force field parameters (as used in the lysozyme tutorial) have been extensively developed, tested and improved over several decades by many scientific groups. This means that you can typically just take a modern protein force field and use it for your simulation without being too worried (although like anything there are exemptions, such as with intrinsically disordered proteins which may require special parameters); you also need to apply it correctly with the appropriate cut-offs and so forth.
In your case, you have a type of molecule that has had far less work having been done upon so as to develop and validate force field parameters. Combine that with the somewhat exotic nature of dyes and the problems this causes fixed charge force fields, it makes it much harder to simulate accurately than lysozyme in the tutorial.
Ofcourse. But i need at least some result. Is this .top file readable? Just to see something in GROMACS
No, it’s not a GROMACS topology (rather for use with XPLOR). You’ve used the wrong output from LigParGen.
And as long as you’re aware that whatever preliminary results you see with these parameters could easily be completely wrong and therefore a waste of time/resources, that’s all I was trying to get across.
Well
I have too much different output files from LigParGen
Is they can be correct to work?
Yes, I’ve used it to generate small molecule OPLS force field parameters before simulations in GROMACS.
If you’re not sure what different files are, what they do in GROMACS, and which you need for your simulation then I suggest completing a couple of the other of Justin’s tutorials (e.g. the protein ligand one) to get to grips with these fundamentals.
Thanks!
Can you share this tutorials?
You linked to one of them above. They’re all at mdtutorials.com/gmx
Thanks
