[gmx-users] Regarding Unknown cmap torsion between atoms

Tue Aug 22 08:19:38 CEST 2017

Hi,

Your description is too confused to follow. Your use of the words solvent
and solute is unclear. pdb2gmx will never make a cmap that goes outside a
moleculetype.

If one use of pdb2gmx made a cmap and the other did not, then they were
fundamentally different. If you don't know what was different, then you
aren't doing science because you don't know what your method was. If so,
start again and keep a record in a shell script this time.

Mark

On Tue, Aug 22, 2017 at 8:05 AM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> 1] in the line 8231 [ Unknown cmap torsion between atoms 8 10 12 15 18] it
> is the diglycine peptide molecule only, it is stating the atomic numbers of
> the diglycine molecule (8,10,12,15) and solute molecule (18)....
> 2] but one more problem is the Diglycine nitrogen and the solute containing
> nitrogen are labelled as same (as N only)...
> ie., atoms 8,10,12,15 (here atom 10 is N, and other atoms are  C, CA)
> belong to diglycine and atom 18 belong to solute molecule of atom N, and
> hence i am getting the error...i hope so....(But with other system tht i
> ran had no [cmap] in topology and the atoms in the solute were labelled
> differently....and ran correctly..)
> 3] So can  i remove/delete the [cmap] line .... (i tried removing cmap line
> in topology..and thn with gmx grompp option it is workin fine..) does that
> cause any error/manipulating the topology..etc..?? can i proceed removing
> [cmap].... is thr any harm..?
> 4] I tried also with removing the last coloumn in [cmap] ie., removing 18,1
> of am,funct..since as i told above the atom 18 is of the solute nitrogen
> molecule which is labelled as same in the .rtp file in charmmFF, which is
> causing the problems....since the gmx grompp is trying to bond wiht the
> atom 18 N  which is solute and not Diglycine (since both N's are labelled
> same)
> [ cmap ]
> ;  ai    aj    ak    al    am funct
>     8    10    12    15    18     1
> and edited and got it as:-
>
> [ cmap ]
> ;  ai    aj    ak    al
>     8    10    12    15
> and thn now if i run gmx grompp -f min.mdp -c mixture.gro -p topol.top -o
> min.tpr
>  it is showing:-
>  WARNING 1 [file topol.top, line 8231]:
>   Too few parameters on line (source file
>
> /home/dilip/Downloads/gromacs-2016.2/src/gromacs/gmxpreprocess/toppush.cpp,
> line 2198)
> So i tried with gmx grompp -f min.mdp -c mixture.gro -p topol.top -o
> min.tpr -maxwarn 2 , and now it is working fine...
>
> So i have tried with different options..and i have discussed what i have
> got..but are they the correct way...to proceed..??
>
> Any suggestions are welcome...
>
> Thank you...
>
>
> <https://mailtrack.io/> Sent with Mailtrack
> <
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> >
>
> On Mon, Aug 21, 2017 at 11:14 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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
> > > > > --
> > > > > Gromacs Users mailing list
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> > > --
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> > >
> > > DILIP.H.N
> > > Ph.D Student
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> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
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