[gmx-users] Regarding Unknown cmap torsion between atoms

Dilip H N cy16f01.dilip at nitk.edu.in
Mon Aug 21 18:33:35 CEST 2017

I have created a peptide from chimera software and got the pdb file, and i
have added solvents to it the resultant is mixture.gro, and used gmx
pdb2gmx to generate the topology using charmm36 FF. I got the topology
correct, but nw if i give the command for energy minimization :-
gmx grompp -f min.mdp -c mixture.gro -p topol.top -o min.tpr

I am getting error as:-

NOTE 1 [file min.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 -1490567170
Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations

ERROR 1 [file topol.top, line 8231]:
  Unknown cmap torsion between atoms 8 10 12 15 18

There was 1 note
Program:     gmx grompp, version 2016.3
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1622)

Fatal error:
There was 1 error in input file(s)

1] What is this cmap all about..??
2] How do i correct this error..?

Any suggestions will be helpful...

Thank you...

With Best Regards,

Ph.D Student

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