[gmx-users] Regarding Unknown cmap torsion between atoms

[Mark Abraham]

Hi,

If your procedure for the two systems was actually the same, then the error
does not come from your solute. Unfortunately only you know what is on line
8231... Work out what you did differently, e.g. by doing it again and
making sure you do it the same way.

Mark

On Mon, Aug 21, 2017 at 7:27 PM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> 1] I created Diglycine peptide from chimera software, and got the .pdb
> file, added two different solvents (A, B) and made two different systems
> say, A-(Diglycine+solvent1), B-(Diglycine+solvent2). I generated the
> topology file from charmm36 FF by gmx pdb2gmx process for both the systems
> A and B correctly (but in system A there is no [ cmap ] line in topology,
> but system B has [ cmap ] in topology).. Why is this in one system i am
> getting but in other i am not..?  Is there any error...or what is it...
>
> 2] And  during gmx grompp  -f min.mdp -c mixture.gro -p topol.top -o
> min.tpr
>
> for system A (whr there is no [cmap] in topology), the gmx grompp command
> works well...
> But for system B (which has [cmap] in topology), the error comes as:-
>
> > ERROR 1 [file topol.top, line 8231]:
> >  Unknown cmap torsion between atoms 8 10 12 15 18
>
> How can i solve this ...??
>
> Thank you...
>
>
> On Mon, Aug 21, 2017 at 10:18 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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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>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
> --
> Gromacs Users mailing list
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