[gmx-users] Regarding Unknown cmap torsion between atoms

[Mark Abraham]

Hi,

On Mon, Aug 21, 2017 at 6:33 PM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> Hello,
> 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..??
>

That's part of how the CHARMM force field works for modelling peptides. You
should have a basic understanding of that from your background reading that
led to the choice of this force field.


> 2] How do i correct this error..?
>

Whether you can do so depends whether chimera has generated a structure
that has a valid CHARMM36 representation, ie there exists a CMAP definition
for the types of those atoms.

Mark


> Any suggestions will be helpful...
>
> Thank you...
>
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
> --
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