[gmx-users] Regarding Unknown cmap torsion between atoms

Tue Aug 22 08:40:19 CEST 2017

Hello,
1] it is the solute+Diglycine which is the constituting the mixture...
2] the method to create the system for both were the same...
the commands are...
gmx editconf -f Diglycinechimera2.gro -o Diglybox.gro -c -box x y z
(generating the box)
gmx insert-molecules -f Diglybox.gro -ci abc.gro -nmol 10 -o Dglyabc.gro
and for other system, gmx insert-molecules -f Diglybox.gro -ci def.gro
-nmol 10 -o Dglydef.gro (adding the solute molecules and getting the final
system)...
here the two solute .gro files are abc.gro and def.gro....and i have
followed the same procedure...
and thn gmx pdb2gmx -f Dglyabc.gro (or) gmx pdb2gmx -f Dglydef.gro...there
is [cmap] option in one topology file and in other topology there is no
[cmap] option...

How is it different thn..??

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On Tue, Aug 22, 2017 at 11:49 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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
> > <
> > https://mailtrack.io/install?source=signature&lang=en&
> referral=cy16f01.dilip at nitk.edu.in&idSignature=22
> > >
> >
> > 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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> >
> > DILIP.H.N
> > Ph.D Student
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student