[gmx-users] Regarding Unknown cmap torsion between atoms
Mark Abraham
mark.j.abraham at gmail.com
Wed Aug 23 15:31:16 CEST 2017
Hi,
I don't understand whether you think diglycine is your solvent or your
solute.
Mark
On Tue, Aug 22, 2017 at 8:40 AM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:
> 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..??
>
>
>
>
>
>
> <https://mailtrack.io/> Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22
> >
>
> 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
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