GROMACS version: VERSION 5.1.1
GROMACS modification: Yes/No
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Dear experts,
While using ions.tpr command line I am facing errors. Forcefield used: charmm36-mar2019.ff
Command line:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
Ignoring obsolete mdp entry ‘title’
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
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 2813366769
WARNING 1 [file drg.prm, line 4]:
Overriding Bond parameters.
old: 0.1475 234304 0.1475 234304
new: CG2O1 CG2R51 1 0.14750000 251040.00
WARNING 2 [file drg.prm, line 17]:
Overriding U-B parameters.
old: 122 376.56 0 0 122 376.56 0 0
new: CG2R51 CG2O1 OG2D1 5 121.000000 251.040000 0.00000000 0.00
WARNING 3 [file drg.prm, line 19]:
Overriding U-B parameters.
old: 130 292.88 0 0 130 292.88 0 0
new: CG2O1 CG2R51 CG2R51 5 130.000000 383.254400 0.00000000 0.00
WARNING 4 [file drg.prm, line 35]:
Overriding Proper Dih. parameters.
Use dihedraltype 9 to allow several multiplicity terms. Only consecutive
lines are combined. Non-consective lines overwrite each other.
old: 180 7.1128 2 180 7.1128 2
new: OG2D1 CG2O1 CG2R51 CG2R51 9 180.000000 4.184000 2
Generated 100032 of the 100128 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 65937 of the 100128 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein’
Excluding 3 bonded neighbours molecule type ‘DRG’
NOTE 2 [file topol.top, line 61631]:
System has non-zero total charge: 3.000004
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.
Program gmx grompp, VERSION 5.1.1
Source code file: /home/cl_dop/Downloads/gromacs/gromacs-5.1.1/src/gromacs/gmxpreprocess/grompp.c, line: 605
Fatal error:
number of coordinates in coordinate file (solv.gro, 55333)
does not match topology (topol.top, 6512)
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
Please help!