GROMACS version:2018
GROMACS modification: Yes/No
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Kindly help me deal with the mismatch below. Am using Gromacs 2018 running a gromacs tutorial 5. The chloride ions in the topol.top file are written as CLA. when doing the energy minimization while maintaining the ion as CL. am told no such moleculetype exists and when i change it to CLA i get a mismatch:
Warning: atom name 33501 in topol.top and solv_ions.gro does not match (CLA - CL)
Warning: atom name 33502 in topol.top and solv_ions.gro does not match (CLA - CL)
Warning: atom name 33503 in topol.top and solv_ions.gro does not match (CLA - CL)
Warning: atom name 33504 in topol.top and solv_ions.gro does not match (CLA - CL)
Warning: atom name 33505 in topol.top and solv_ions.gro does not match (CLA - CL)
Warning: atom name 33506 in topol.top and solv_ions.gro does not match (CLA - CL)
WARNING 1 [file topol.top, line 24633]:
6 non-matching atom names
atom names from topol.top will be used
atom names from solv_ions.gro will be ignored
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are: 163 Protein residues
There are: 7 Other residues
There are: 10288 Water residues
Analysing Protein…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Number of degrees of freedom in T-Coupling group rest is 69651.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 72x72x72, spacing 0.109 0.109 0.109
Estimate for the relative computational load of the PME mesh part: 0.07
This run will generate roughly 3 Mb of data
There was 1 note
There was 1 warning
Program: gmx grompp, version 2018.6
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2406)
Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation