[gmx-users] Regarding Unknown cmap torsion between atoms
Dilip H N
cy16f01.dilip at nitk.edu.in
Tue Aug 22 08:05:04 CEST 2017
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...
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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
> > > > --
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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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