GROMACS modification: Yes
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I have been trying to perform protein-ligand simulations. I have a docked complex from the maestro and saved it in a PDB format and now trying to proceed for MD simulation via gromacs.
command : /usr/local/gromacs/gmx pdb2gmx -f test-lig-covdock.pdb -o test.gro
Here’s the error :
Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 ‘B’ (2662 atoms, 175 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 278 donors and 260 acceptors were found.
There are 326 hydrogen bonds
Will use HISD for residue 184
Will use HISE for residue 222
Will use HISE for residue 285
Will use HISE for residue 293
Program: gmx pdb2gmx, version 2020
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 902)
The residues in the chain ACE167–NMA340 do not have a consistent type. The
first residue has type ‘Protein’, while residue NMA340 is of type ‘Other’.
Either there is a mistake in your chain, or it includes nonstandard residue
names that have not yet been added to the residuetypes.dat file in the GROMACS
library directory. If there are other molecules such as ligands, they should
not have the same chain ID as the adjacent protein chain since it’s a separate