Warnings and Errors in the use of grompp

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1

GROMACS version: 2020.1-Ubuntu-2020.1-1
GROMACS modification: No
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I am new to GROMACS. I used the tutorial for Protein-Ligand Complex MD Simulation provided via http://www.mdtutorials.com/gmx/complex/index.html but while trying to use the grompp command, gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr, the following warnings and errors were encountered.

NOTE 1 [file ions.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.

Setting the LD random seed to 1838392092

WARNING 1 [file unk.prm, line 4]:
Bondtype Bond 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: 0.1381 284512 0.1381 284512
new: CG2RC0 NG2R52 1 0.13700000 317984.00

WARNING 2 [file unk.prm, line 13]:
Bondtype U-B 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: 106.9 602.496 0 0 106.9 602.496 0 0
new: CG2RC0 CG2RC0 NG2R52 5 110.000000 585.760000 0.00000000 0.00

WARNING 3 [file unk.prm, line 14]:
Bondtype U-B 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: 126.9 602.496 0 0 126.9 602.496 0 0
new: NG2R52 CG2RC0 NG2R62 5 122.600000 167.360000 0.00000000 0.00

WARNING 4 [file unk.prm, line 26]:
Bondtype U-B 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: 108 861.904 0 0 108 861.904 0 0
new: CG2R53 NG2R52 CG2RC0 5 108.000000 1213.360000 0.00000000 0.00

WARNING 5 [file unk.prm, line 29]:
Bondtype U-B 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: 126.9 326.352 0 0 126.9 326.352 0 0
new: CG2RC0 NG2R52 HGP2 5 124.900000 209.200000 0.21300000 12552.00

ERROR 1 [file unk.prm, line 37]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 2 [file unk.prm, line 39]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 3 [file unk.prm, line 47]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 4 [file unk.prm, line 48]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 5 [file unk.prm, line 51]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 6 [file unk.prm, line 53]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 7 [file unk.prm, line 54]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations

ERROR 8 [file unk.itp, line 79]:
No default Bond types

ERROR 9 [file unk.itp, line 80]:
No default Bond types

ERROR 10 [file unk.itp, line 291]:
No default U-B types

ERROR 11 [file unk.itp, line 322]:
No default U-B types

ERROR 12 [file unk.itp, line 323]:
No default U-B types

ERROR 13 [file unk.itp, line 349]:
No default U-B types

ERROR 14 [file unk.itp, line 350]:
No default U-B types

ERROR 15 [file unk.itp, line 351]:
No default U-B types

ERROR 16 [file unk.itp, line 425]:
No default Proper Dih. types

ERROR 17 [file unk.itp, line 426]:
No default Proper Dih. types

ERROR 18 [file unk.itp, line 427]:
No default Proper Dih. types

ERROR 19 [file unk.itp, line 432]:
No default Proper Dih. types

ERROR 20 [file unk.itp, line 433]:
No default Proper Dih. types

ERROR 21 [file unk.itp, line 526]:
No default Proper Dih. types

ERROR 22 [file unk.itp, line 527]:
No default Proper Dih. types

ERROR 23 [file unk.itp, line 528]:
No default Proper Dih. types

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘UNK’
Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 2 [file topol.top, line 44221]:
System has non-zero total charge: -3.000000
Total charge should normally be an integer.

There were 2 notes

There were 5 warnings

Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1928)

Fatal error:
There were 23 errors in input file(s)

I clearly do not have any idea on what to do now. Please can I get help/assistance on what to do to solve this problem?

Thanks

2

This is a common problem that has been discussed numerous times - Google can probably tell you.

What’s happening is the ParamChem server has an older version of CGenFF than what we provide with the CHARMM36 port, so you get parameter conflicts. grompp finds multiple copies of the parameters (in ffbonded.itp and in your ligand’s parameter file, and throws the warnings. Remove the duplicate parameters from your .prm file.

The missing parameters are more mysterious and suggest that your ligand has interactions totally unknown to the force field. This shouldn’t happen with a CGenFF-generated topology, but you’re not actually working with the tutorial system so I can’t say what’s going on. But the solution is to define the missing parameters in your topology.

3

Thanks a lot, @jalemkul. Your reply was very helpful. I have been able to continue the MD Simulation after attending to the errors.

4

Hi AglowRaph
Can u plz tell me how did u resolved the error. I used cgenff server for topology generation and i still get the first two error u mentioned.
thank you

5

Dr. Lemkul , I generated topologies of ligand using cgenff server and it gives no error or warning. but trying to use the grompp command, *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr., I get the same erros which Mr. AglowRaph has got ( error with line 4 of .prm file and also 13 errors in the .itp file. Can you plz help me to rectify this?
thank you in advance.

6

I do not know what the resolution to the original problem was because @AglowRaph did not say what the fix was, but I maintain that the solution to these errors is as follows:

  1. Duplicate parameter: remove the offending line(s) from the ligand’s .prm file
  2. Missing parameter: you didn’t #include the .prm file appropriately