No default Bond types, U-B types and Proper Dih. types

User discussions
1

GROMACS version: 2022.3-Homebrew
GROMACS modification: NO

Hi there,

I am simulating polymer-nucleic acid complex.When trying to grompp with ions.mdp producing lots (1847 ERRORS) of errors related with No default Bond types, No default U-B types and No default Proper Dih. types.

Error file attached.

image
image934×848 109 KB

❯ gmx grompp -f ions.mdp -c N30_solv.gro -p topol.top -o ions.tpr
:-) GROMACS - gmx grompp, 2022.3-Homebrew (-:

Executable: /usr/local/bin/…/Cellar/gromacs/2022.3/bin/gmx
Data prefix: /usr/local/bin/…/Cellar/gromacs/2022.3
Working dir: /Users/deshdeepak/Desktop/workspace/Polymers/Oligomer_NAPA/NAPA30/Polymer_processing
Command line:
gmx grompp -f ions.mdp -c N30_solv.gro -p topol.top -o ions.tpr

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 -169230475

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

Generated 117519 of the 167910 1-4 parameter combinations

ERROR 1 [file topol.top, line 1029]:
No default Bond types

ERROR 2 [file topol.top, line 1035]:
No default Bond types

ERROR 9 [file topol.top, line 1071]:
No default Bond types

ol.top, line 5706]:
No default U-B types

ERROR 627 [file topol.top, line 5722]:
No default U-B types

ERROR 1737 [file topol.top, line 8447]:
No default Proper Dih. types

ERROR 1738 [file topol.top, line 8448]:
No default Proper Dih. types

ERROR 1739 [file topol.top, line 8450]:
No default Proper Dih. types

ERROR 1740 [file topol.top, line 8451]:
No default Proper Dih. types

ERROR 1741 [file topol.top, line 8452]:
No default Proper Dih. types

ERROR 1742 [file topol.top, line 8453]:
No default Proper Dih. types

ERROR 1743 [file topol.top, line 8454]:
No default Proper Dih. types

ERROR 1744 [file topol.top, line 8467]:
No default Proper Dih. types

ERROR 1745 [file topol.top, line 8471]:
No default Proper Dih. types

ERROR 1746 [file topol.top, line 8475]:
No default Proper Dih. types

ERROR 1747 [file topol.top, line 8480]:
No default Proper Dih. types

ERROR 1748 [file topol.top, line 8482]:
No default Proper Dih. types

ERROR 1749 [file topol.top, line 8485]:
No default Proper Dih. types

ERROR 1750 [file topol.top, line 8486]:
No default Proper Dih. types

ERROR 1751 [file topol.top, line 8487]:
No default Proper Dih. types

ERROR 1752 [file topol.top, line 8488]:
No default Proper Dih. types

ERROR 1753 [file topol.top, line 8493]:
No default Proper Dih. types

ERROR 1754 [file topol.top, line 8494]:
No default Proper Dih. types

ERROR 1755 [file topol.top, line 8496]:
No default Proper Dih. types

ERROR 1756 [file topol.top, line 8498]:
No default Proper Dih. types

ERROR 1757 [file topol.top, line 8499]:
No default Proper Dih. types

ERROR 1758 [file topol.top, line 8501]:
No default Proper Dih. types

ERROR 1759 [file topol.top, line 8502]:
No default Proper Dih. types

ERROR 1760 [file topol.top, line 8503]:
No default Proper Dih. types

ERROR 1761 [file topol.top, line 8504]:
No default Proper Dih. types

ERROR 1762 [file topol.top, line 8505]:
No default Proper Dih. types

ERROR 1763 [file topol.top, line 8508]:
No default Proper Dih. types

ERROR 1764 [file topol.top, line 8509]:
No default Proper Dih. types

ERROR 1765 [file topol.top, line 8520]:
No default Proper Dih. types

ERROR 1766 [file topol.top, line 8521]:
No default Proper Dih. types

ERROR 1767 [file topol.top, line 8522]:
No default Proper Dih. types

ERROR 1768 [file topol.top, line 8528]:
No default Proper Dih. types

ERROR 1769 [file topol.top, line 8530]:
No default Proper Dih. types

ERROR 1770 [file topol.top, line 8531]:
No default Proper Dih. types

ERROR 1771 [file topol.top, line 8533]:
No default Proper Dih. types

ERROR 1772 [file topol.top, line 8534]:
No default Proper Dih. types

ERROR 1773 [file topol.top, line 8535]:
No default Proper Dih. types

ERROR 1774 [file topol.top, line 8537]:
No default Proper Dih. types

ERROR 1775 [file topol.top, line 8538]:
No default Proper Dih. types

ERROR 1776 [file topol.top, line 8539]:
No default Proper Dih. types

ERROR 1777 [file topol.top, line 8540]:
No default Proper Dih. types

ERROR 1778 [file topol.top, line 8550]:
No default Proper Dih. types

ERROR 1779 [file topol.top, line 8552]:
No default Proper Dih. types

ERROR 1780 [file topol.top, line 8555]:
No default Proper Dih. types

ERROR 1781 [file topol.top, line 8556]:
No default Proper Dih. types

ERROR 1782 [file topol.top, line 8557]:
No default Proper Dih. types

ERROR 1783 [file topol.top, line 8558]:
No default Proper Dih. types

ERROR 1784 [file topol.top, line 8563]:
No default Proper Dih. types

ERROR 1785 [file topol.top, line 8564]:
No default Proper Dih. types

ERROR 1786 [file topol.top, line 8566]:
No default Proper Dih. types

ERROR 1787 [file topol.top, line 8568]:
No default Proper Dih. types

ERROR 1788 [file topol.top, line 8569]:
No default Proper Dih. types

ERROR 1789 [file topol.top, line 8571]:
No default Proper Dih. types

ERROR 1790 [file topol.top, line 8572]:
No default Proper Dih. types

ERROR 1791 [file topol.top, line 8573]:
No default Proper Dih. types

ERROR 1792 [file topol.top, line 8574]:
No default Proper Dih. types

ERROR 1793 [file topol.top, line 8575]:
No default Proper Dih. types

ERROR 1794 [file topol.top, line 8578]:
No default Proper Dih. types

ERROR 1795 [file topol.top, line 8579]:
No default Proper Dih. types

ERROR 1796 [file topol.top, line 8590]:
No default Proper Dih. types

ERROR 1797 [file topol.top, line 8591]:
No default Proper Dih. types

ERROR 1798 [file topol.top, line 8592]:
No default Proper Dih. types

ERROR 1799 [file topol.top, line 8598]:
No default Proper Dih. types

ERROR 1800 [file topol.top, line 8600]:
No default Proper Dih. types

ERROR 1801 [file topol.top, line 8601]:
No default Proper Dih. types

ERROR 1802 [file topol.top, line 8603]:
No default Proper Dih. types

ERROR 1803 [file topol.top, line 8604]:
No default Proper Dih. types

ERROR 1804 [file topol.top, line 8605]:
No default Proper Dih. types

ERROR 1805 [file topol.top, line 8607]:
No default Proper Dih. types

ERROR 1806 [file topol.top, line 8608]:
No default Proper Dih. types

ERROR 1807 [file topol.top, line 8609]:
No default Proper Dih. types

ERROR 1808 [file topol.top, line 8610]:
No default Proper Dih. types

ERROR 1809 [file topol.top, line 8611]:
No default Proper Dih. types

ERROR 1810 [file topol.top, line 8613]:
No default Proper Dih. types

ERROR 1811 [file topol.top, line 8616]:
No default Proper Dih. types

ERROR 1812 [file topol.top, line 8620]:
No default Proper Dih. types

ERROR 1813 [file topol.top, line 8621]:
No default Proper Dih. types

ERROR 1814 [file topol.top, line 8622]:
No default Proper Dih. types

ERROR 1815 [file topol.top, line 8625]:
No default Proper Dih. types

ERROR 1816 [file topol.top, line 8626]:
No default Proper Dih. types

ERROR 1817 [file topol.top, line 8629]:
No default Proper Dih. types

ERROR 1818 [file topol.top, line 8630]:
No default Proper Dih. types

ERROR 1819 [file topol.top, line 8632]:
No default Proper Dih. types

ERROR 1820 [file topol.top, line 8634]:
No default Proper Dih. types

ERROR 1821 [file topol.top, line 8637]:
No default Proper Dih. types

ERROR 1822 [file topol.top, line 8638]:
No default Proper Dih. types

ERROR 1823 [file topol.top, line 8639]:
No default Proper Dih. types

ERROR 1824 [file topol.top, line 8640]:
No default Proper Dih. types

ERROR 1825 [file topol.top, line 8645]:
No default Proper Dih. types

ERROR 1826 [file topol.top, line 8646]:
No default Proper Dih. types

ERROR 1827 [file topol.top, line 8648]:
No default Proper Dih. types

ERROR 1828 [file topol.top, line 8650]:
No default Proper Dih. types

ERROR 1829 [file topol.top, line 8651]:
No default Proper Dih. types

ERROR 1830 [file topol.top, line 8653]:
No default Proper Dih. types

ERROR 1831 [file topol.top, line 8654]:
No default Proper Dih. types

ERROR 1832 [file topol.top, line 8655]:
No default Proper Dih. types

ERROR 1833 [file topol.top, line 8656]:
No default Proper Dih. types

ERROR 1834 [file topol.top, line 8657]:
No default Proper Dih. types

ERROR 1835 [file topol.top, line 8660]:
No default Proper Dih. types

ERROR 1836 [file topol.top, line 8661]:
No default Proper Dih. types

ERROR 1837 [file topol.top, line 8672]:
No default Proper Dih. types

ERROR 1838 [file topol.top, line 8673]:
No default Proper Dih. types

ERROR 1839 [file topol.top, line 8674]:
No default Proper Dih. types

ERROR 1840 [file topol.top, line 8680]:
No default Proper Dih. types

ERROR 1841 [file topol.top, line 8682]:
No default Proper Dih. types

ERROR 1842 [file topol.top, line 8683]:
No default Proper Dih. types

ERROR 1843 [file topol.top, line 8685]:
No default Proper Dih. types

ERROR 1844 [file topol.top, line 8686]:
No default Proper Dih. types

ERROR 1845 [file topol.top, line 8687]:
No default Proper Dih. types

ERROR 1846 [file topol.top, line 8689]:
No default Proper Dih. types

ERROR 1847 [file topol.top, line 8690]:
No default Proper Dih. types

Excluding 3 bonded neighbours molecule type ‘Other’

Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 2 [file topol.top, line 8780]:
System has non-zero total charge: 0.180001
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 2022.3-Homebrew
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2172)

Fatal error:
There were 1847 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

~/Desktop/workspace/Polymers/Oligomer_NAPA/NAPA30/Polymer_processing
❯ clear

~/Desktop/workspace/Polymers/Oligomer_NAPA/NAPA30/Polymer_processing
❯ gmx grompp -f ions.mdp -c N30_solv.gro -p topol.top -o ions.tpr
:-) GROMACS - gmx grompp, 2022.3-Homebrew (-:

Executable: /usr/local/bin/…/Cellar/gromacs/2022.3/bin/gmx
Data prefix: /usr/local/bin/…/Cellar/gromacs/2022.3
Working dir: /Users/deshdeepak/Desktop/workspace/Polymers/Oligomer_NAPA/NAPA30/Polymer_processing
Command line:
gmx grompp -f ions.mdp -c N30_solv.gro -p topol.top -o ions.tpr

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 786422779

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

Generated 117519 of the 167910 1-4 parameter combinations

ERROR 1 [file topol.top, line 1029]:
No default Bond types

ERROR 2 [file topol.top, line 1035]:
No default Bond types

ERROR 3 [file topol.top, line 1038]:
No default Bond types

ERROR 4 [file topol.top, line 1042]:
No default Bond types

ERROR 5 [file topol.top, line 1046]:
No default Bond types

ERROR 6 [file topol.top, line 1047]:
No default Bond types

ERROR 7 [file topol.top, line 1057]:
No default Bond types

ERROR 8 [file topol.top, line 1068]:
No default Bond types

ERROR 9 [file topol.top, line 1071]:
No default Bond types

ERROR 10 [file topol.top, line 1075]:
No default Bond types

ERROR 11 [file topol.top, line 1079]:
No default Bond types

ERROR 12 [file topol.top, line 1080]:
No default Bond types

ERROR 13 [file topol.top, line 1090]:
No default Bond types

ERROR 14 [file topol.top, line 1101]:
No default Bond types

ERROR 15 [file topol.top, line 1104]:
No default Bond types

ERROR 16 [file topol.top, line 1108]:
No default Bond types

ERROR 17 [file topol.top, line 1112]:
No default Bond types

ERROR 18 [file topol.top, line 1113]:
No default Bond types

ERROR 19…SO ON…

ERROR 1847 [file topol.top, line 8690]:
No default Proper Dih. types

Excluding 3 bonded neighbours molecule type ‘Other’

Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 2 [file topol.top, line 8780]:
System has non-zero total charge: 0.180001
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 2022.3-Homebrew
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2172)

Fatal error:
There were 1847 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
topol.top (250.8 KB)
ions.mdp (1.0 KB)

2

You likely generated a topology that has new CGenFF parameters that the molecule requires. You haven’t provided them, so you get errors that they are missing. Check the original .str file and then the output of whatever conversion you did between CHARMM and GROMACS.

Also note that your terminal residues are chemically nonsensical because they have a net +0.09e charge. You need to build appropriate terminal residues.

3

Ok sir , but I have not used CGenFF server rather I had added them using pdb2gmx by preparing the RTP file for this molecule by modifying the CHARMM36 ff files.

Sir ,As you answered earlier about the generation of new CGenFF parameters in the topology file ,so now my question is how to IDENTIFY which parameters are new from this topology file?

Secondly, can you explain why my terminal residues are chemically non-sensical ? I think we can balance this charge during addition of appropriate ions . Could you please give insights on this.

4

If they are in the .str file produced by the CGenFF server, they are nonstandard parameters that are new to your species (i.e. not in the parent force field, thus you must supply them).