Error in ion neutralization step

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1

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I am encountering an error in ion neutralization step for DNA attached with modified cholesterol. I generated the modified cholesterol using the cgenff and charmm2gmx.

gmx grompp -f ions.mdp -c new_solv.gro -p topol.top -o ions.tpr
:-) GROMACS - gmx grompp, 2023.3 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /data/nabanita/Feb_test
Command line:
gmx grompp -f ions.mdp -c new_solv.gro -p topol.top -o ions.tpr

Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘ns_type’

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 -609499657

Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1

Generated 117432 of the 167910 1-4 parameter combinations

ERROR 1 [file topol_DNA_chain_D.itp, line 540]:
No default Bond types

ERROR 2 [file topol_DNA_chain_D.itp, line 949]:
No default Bond types

ERROR 3 [file topol_DNA_chain_D.itp, line 2383]:
No default U-B types

ERROR 4 [file topol_DNA_chain_D.itp, line 3126]:
No default U-B types

ERROR 5 [file topol_DNA_chain_D.itp, line 3127]:
No default U-B types

ERROR 6 [file topol_DNA_chain_D.itp, line 3128]:
No default U-B types

ERROR 7 [file topol_DNA_chain_D.itp, line 3129]:
No default U-B types

ERROR 8 [file topol_DNA_chain_D.itp, line 3142]:
No default U-B types

ERROR 9 [file topol_DNA_chain_D.itp, line 3201]:
No default U-B types

ERROR 10 [file topol_DNA_chain_D.itp, line 3370]:
No default Proper Dih. types

ERROR 11 [file topol_DNA_chain_D.itp, line 3371]:
No default Proper Dih. types

ERROR 12 [file topol_DNA_chain_D.itp, line 3372]:
No default Proper Dih. types

ERROR 13 [file topol_DNA_chain_D.itp, line 4449]:
No default Proper Dih. types

ERROR 14 [file topol_DNA_chain_D.itp, line 4450]:
No default Proper Dih. types

ERROR 15 [file topol_DNA_chain_D.itp, line 4451]:
No default Proper Dih. types

ERROR 16 [file topol_DNA_chain_D.itp, line 4452]:
No default Proper Dih. types

ERROR 17 [file topol_DNA_chain_D.itp, line 4453]:
No default Proper Dih. types

ERROR 18 [file topol_DNA_chain_D.itp, line 4454]:
No default Proper Dih. types

ERROR 19 [file topol_DNA_chain_D.itp, line 4455]:
No default Proper Dih. types

ERROR 20 [file topol_DNA_chain_D.itp, line 4456]:
No default Proper Dih. types

ERROR 21 [file topol_DNA_chain_D.itp, line 4457]:
No default Proper Dih. types

ERROR 22 [file topol_DNA_chain_D.itp, line 4469]:
No default Proper Dih. types

ERROR 23 [file topol_DNA_chain_D.itp, line 4472]:
No default Proper Dih. types

ERROR 24 [file topol_DNA_chain_D.itp, line 4475]:
No default Proper Dih. types

ERROR 25 [file topol_DNA_chain_D.itp, line 4476]:
No default Proper Dih. types

ERROR 26 [file topol_DNA_chain_D.itp, line 4536]:
No default Proper Dih. types

ERROR 27 [file topol_DNA_chain_D.itp, line 4537]:
No default Proper Dih. types

ERROR 28 [file topol_DNA_chain_D.itp, line 4538]:
No default Proper Dih. types

ERROR 29 [file topol_DNA_chain_D.itp, line 4544]:
No default Proper Dih. types

ERROR 30 [file topol_DNA_chain_D.itp, line 4551]:
No default Proper Dih. types

ERROR 31 [file topol_DNA_chain_D.itp, line 4557]:
No default Proper Dih. types

ERROR 32 [file topol_DNA_chain_D.itp, line 4558]:
No default Proper Dih. types

ERROR 33 [file topol_DNA_chain_D2.itp, line 534]:
No default Bond types

ERROR 34 [file topol_DNA_chain_D2.itp, line 934]:
No default Bond types

ERROR 35 [file topol_DNA_chain_D2.itp, line 2363]:
No default U-B types

ERROR 36 [file topol_DNA_chain_D2.itp, line 3086]:
No default U-B types

ERROR 37 [file topol_DNA_chain_D2.itp, line 3087]:
No default U-B types

ERROR 38 [file topol_DNA_chain_D2.itp, line 3088]:
No default U-B types

ERROR 39 [file topol_DNA_chain_D2.itp, line 3089]:
No default U-B types

ERROR 40 [file topol_DNA_chain_D2.itp, line 3102]:
No default U-B types

ERROR 41 [file topol_DNA_chain_D2.itp, line 3161]:
No default U-B types

ERROR 42 [file topol_DNA_chain_D2.itp, line 3330]:
No default Proper Dih. types

ERROR 43 [file topol_DNA_chain_D2.itp, line 3331]:
No default Proper Dih. types

ERROR 44 [file topol_DNA_chain_D2.itp, line 3332]:
No default Proper Dih. types

ERROR 45 [file topol_DNA_chain_D2.itp, line 4383]:
No default Proper Dih. types

ERROR 46 [file topol_DNA_chain_D2.itp, line 4384]:
No default Proper Dih. types

ERROR 47 [file topol_DNA_chain_D2.itp, line 4385]:
No default Proper Dih. types

ERROR 48 [file topol_DNA_chain_D2.itp, line 4386]:
No default Proper Dih. types

ERROR 49 [file topol_DNA_chain_D2.itp, line 4387]:
No default Proper Dih. types

ERROR 50 [file topol_DNA_chain_D2.itp, line 4388]:
No default Proper Dih. types

ERROR 51 [file topol_DNA_chain_D2.itp, line 4389]:
No default Proper Dih. types

ERROR 52 [file topol_DNA_chain_D2.itp, line 4390]:
No default Proper Dih. types

ERROR 53 [file topol_DNA_chain_D2.itp, line 4391]:
No default Proper Dih. types

ERROR 54 [file topol_DNA_chain_D2.itp, line 4403]:
No default Proper Dih. types

ERROR 55 [file topol_DNA_chain_D2.itp, line 4406]:
No default Proper Dih. types

ERROR 56 [file topol_DNA_chain_D2.itp, line 4409]:
No default Proper Dih. types

ERROR 57 [file topol_DNA_chain_D2.itp, line 4410]:
No default Proper Dih. types

ERROR 58 [file topol_DNA_chain_D2.itp, line 4470]:
No default Proper Dih. types

ERROR 59 [file topol_DNA_chain_D2.itp, line 4471]:
No default Proper Dih. types

ERROR 60 [file topol_DNA_chain_D2.itp, line 4472]:
No default Proper Dih. types

ERROR 61 [file topol_DNA_chain_D2.itp, line 4478]:
No default Proper Dih. types

ERROR 62 [file topol_DNA_chain_D2.itp, line 4485]:
No default Proper Dih. types

ERROR 63 [file topol_DNA_chain_D2.itp, line 4491]:
No default Proper Dih. types

ERROR 64 [file topol_DNA_chain_D2.itp, line 4492]:
No default Proper Dih. types

ERROR 65 [file topol_DNA_chain_D3.itp, line 1213]:
No default Bond types

ERROR 66 [file topol_DNA_chain_D3.itp, line 5350]:
No default U-B types

ERROR 67 [file topol_DNA_chain_D3.itp, line 7598]:
No default Proper Dih. types

ERROR 68 [file topol_DNA_chain_D3.itp, line 7599]:
No default Proper Dih. types

ERROR 69 [file topol_DNA_chain_D3.itp, line 7600]:
No default Proper Dih. types

Excluding 3 bonded neighbours molecule type ‘DNA_chain_D’

Excluding 3 bonded neighbours molecule type ‘DNA_chain_D2’

Excluding 3 bonded neighbours molecule type ‘DNA_chain_D3’

Excluding 3 bonded neighbours molecule type ‘DNA_chain_D4’

Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 2 [file topol.top, line 52]:
System has non-zero total charge: -92.159992
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.

There were 2 NOTEs

Program: gmx grompp, version 2023.3
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2198)

Fatal error:
There were 69 errors in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

Thank you in advance

2

Hi, the error is not in neutralization - your topology simply doesn’t include parameters for the selected combinations of atomtypes. If it’s the cholesterol-NA conjugate, that’s expected, as you should transfer them from an external parametrization (say, CGenFF).

You might find helpful some functions to show which parameters are missing, and perhaps to read parameters from an external topology file if you have one.

3

@milosz.wieczor I have already added the parameters for modified cholesterol in .rtp file as well as ffbonded.itp file.

4

Then you can use the function I linked to above to list which parameters are missing according to gmx grompp, perhaps different ones are missing, although I have no idea why would they be.