[gmx-users] Regarding Unknown cmap torsion between atoms

[Dilip H N]

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