[gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093)
swati rana
swati.rana088 at gmail.com
Sat Apr 13 10:57:14 CEST 2013
Hi,
I am facing this issue with the energy minimization. The following is the
output when i try to pack the lipids around the protein:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 20000
Step= 14, Dmax= 1.2e-06 nm, Epot= 3.37981e+20 Fmax= inf, atom=
147
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 10 (whichmay not be possible for your system). It
stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.
i know this is not an error but the potential energy is very high i went
through the mailing list as well but could not get the answer for my
question.
THERE IS AN OVERLAP IN POPC AND LIGAND. WHEN I SELECT MY LIGAND IN PYMOL
simultaneously ONE POPC ATOM ALSO GETS SELECTED and i understand that is
the problem but what should be done to correct this. i tried to reposition
the ligand and copied its coordinates in the last that worked in system.gro
file but again when system_inflated.gro file was generated again there was
an overlap. please tell how to solve this issue. how to correct this
overlap thing. Do i have to number each atom from the start to end in a
flow like instead of popc 1st molecule to be numbered as 1 should i
renumber it to what was the last for proteins.
THANKS in advance...
Swati.
On Thu, Mar 21, 2013 at 11:41 AM, Emanuel Birru <Emanuel.Birru at monash.edu>wrote:
> So the problem is so simple then. You use different atom name in you gro
> file than in yout topology. You have to use the same atom names in both.
>
> If you are confident in your gro file change the topology to OW1, HW2 and
> HW3 that will solve the problem.
>
> Cheers,
> EB
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of swati rana
> Sent: Thursday, 21 March 2013 5:00 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] number of coordinates in coordinate file
> (system.gro, 10019) does not match topology (topol.top, 17093)
>
> yes its POPC at the top and SOL at the bottom. But the atoms names are not
> same that is the problem. ...
>
> I am pasting the part of the gro file from where the problem has started.
> At 129 position the atom name is OW1 where as in topol file it is OW.
> Please guide me what should be done.
>
> 128POP C50 6654 4.864 -0.191 3.551
> 128POP CA1 6655 5.688 0.221 3.577
> 128POP CA2 6656 5.641 0.199 3.433
> 129SOL OW1 6657 5.223 1.492 0.817
> 129SOL HW2 6658 5.129 1.491 0.783
> 129SOL HW3 6659 5.277 1.423 0.769
> 130SOL OW1 6660 3.403 3.481 1.092
> 130SOL HW2 6661 3.313 3.523 1.107
> 130SOL HW3 6662 3.391 3.383 1.076
> 131SOL OW1 6663 3.852 2.274 0.985
> 131SOL HW2 6664 3.949 2.292 0.969
> 131SOL HW3 6665 3.811 2.353 1.030
> 132SOL OW1 6666 2.283 4.574 6.734
> 132SOL HW2 6667 2.231 4.637 6.675
> 132SOL HW3 6668 2.364 4.543 6.685
> 133SOL OW1 6669 2.569 2.428 5.841
> 133SOL HW2 6670 2.623 2.469 5.914
> 133SOL HW3 6671 2.629 2.372 5.783
> 134SOL OW1 6672 4.126 0.240 5.606
> 134SOL HW2 6673 4.180 0.312 5.562
> 134SOL HW3 6674 4.182 0.159 5.620
> 135SOL OW1 6675 5.968 3.911 5.734
> 135SOL HW2 6676 5.903 3.964 5.679
> 135SOL HW3 6677 6.042 3.878 5.675
> 136SOL OW1 6678 5.884 2.082 0.044
> 136SOL HW2 6679 5.824 2.156 0.076
> 136SOL HW3 6680 5.860 2.060 -0.051
> 137SOL OW1 6681 3.169 2.752 1.170
> 137SOL HW2 6682 3.250 2.714 1.214
> 137SOL HW3 6683 3.169 2.727 1.073
> 138SOL OW1 6684 5.521 5.906 6.408
> 138SOL HW2 6685 5.601 5.848 6.422
> 138SOL HW3 6686 5.480 5.927 6.497
> 139SOL OW1 6687 5.333 3.675 1.289
> 139SOL HW2 6688 5.387 3.677 1.205
> 139SOL HW3 6689 5.338 3.584 1.330
> 140SOL OW1 6690 3.167 5.794 0.240
> 140SOL HW2 6691 3.077 5.820 0.204
> 140SOL HW3 6692 3.237 5.854 0.203
>
> Thanks in advance...
>
> Swati
>
>
> On Thu, Mar 21, 2013 at 11:18 AM, Emanuel Birru <Emanuel.Birru at monash.edu
> >wrote:
>
> > If the atom names in your gro file and in the top file are the same
> > then I suggest to check how the sequence of the atoms looks like in your
> gro file.
> > Is it POPC at the top and the water at the bottom as your topology
> > suggested? If not swap them in the molecule section.
> >
> > [ molecules ]
> > ; molecule name nr.
> > POPC 128 ???
> > SOL 2460 ???
> >
> > Cheers,
> > EB
> >
> >
> > -----Original Message-----
> > From: gmx-users-bounces at gromacs.org
> > [mailto:gmx-users-bounces at gromacs.org]
> > On Behalf Of swati rana
> > Sent: Thursday, 21 March 2013 4:37 PM
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] number of coordinates in coordinate file
> > (system.gro, 10019) does not match topology (topol.top, 17093)
> >
> > Dear Justin,
> >
> > I am facing another problem i.e. IN removing the periodicity of the
> > downloaded popc128a.pdb file.
> >
> > Warning: atom name 6673 in topol_popc.top and popc128a.gro does not
> > match
> > (HW1 - HW2)
> > Warning: atom name 6674 in topol_popc.top and popc128a.gro does not
> > match
> > (HW2 - HW3)
> > Warning: atom name 6675 in topol_popc.top and popc128a.gro does not
> > match (OW - OW1)
> > Warning: atom name 6676 in topol_popc.top and popc128a.gro does not
> > match
> > (HW1 - HW2)
> > (more than 20 non-matching atom names)
> >
> > WARNING 1 [file topol_popc.top, line 31]:
> > 7380 non-matching atom names
> > atom names from topol_popc.top will be used
> > atom names from popc128a.gro will be ignored
> >
> > This question has been asked by another person as well and in case the
> > solution he suggested worked. But in my case everything in the pdb
> > file is okie though i am getting this error. Please suggest what should
> be done.
> >
> > spc.itp file is like this:
> >
> > [ moleculetype ]
> > ; molname nrexcl
> > SOL 2
> >
> > [ atoms ]
> > ; nr type resnr residue atom cgnr charge mass
> > #ifndef HEAVY_H
> > 1 OW 1 SOL OW 1 -0.82 15.99940
> > 2 H 1 SOL HW1 1 0.41 1.00800
> > 3 H 1 SOL HW2 1 0.41 1.00800
> > #else
> > 1 OW 1 SOL OW 1 -0.82 9.95140
> > 2 H 1 SOL HW1 1 0.41 4.03200
> > 3 H 1 SOL HW2 1 0.41 4.03200
> > #endif
> >
> > #ifndef FLEXIBLE
> > [ settles ]
> > ; OW funct doh dhh
> > 1 1 0.1 0.16330
> >
> > [ exclusions ]
> > 1 2 3
> > 2 1 3
> > 3 1 2
> > #else
> > [ bonds ]
> > ; i j funct length force.c.
> > 1 2 1 0.1 345000 0.1 345000
> > 1 3 1 0.1 345000 0.1 345000
> >
> > [ angles ]
> > ; i j k funct angle force.c.
> > 2 1 3 1 109.47 383 109.47 383
> > #endif
> >
> > And topol file is:
> >
> > ;
> > ; File 'topol_popc.top' was generated
> > ; By user: swati (1000)
> > ; On host: laptop
> > ; At date: Wed Feb 27 14:16:52 2013
> > ;
> > ; This is your topology file
> > ;
> > ; Include chain topologies
> > #include "gromos43a1_lipid.ff/forcefield.itp"
> >
> > ; Include ligand toplogy
> > #include "gromos43a1_lipid.ff/ligand.itp"
> >
> > ; Include lipid topology
> > #include "popc.itp"
> >
> > ; Include water topology
> > #include "gromos43a1_lipid.ff/spc.itp"
> >
> > ; Include ion topologies
> > #include "gromos43a1_lipid.ff/ions.itp"
> >
> > ; System specifications
> > [ system ]
> > 128-Lipid POPC Bilayer
> >
> > [ molecules ]
> > ; molecule name nr.
> > POPC 128
> > SOL 2460
> >
> > Thanks in advance.
> >
> > With Regards,
> > Swati.
> >
> >
> >
> > On Mon, Mar 4, 2013 at 12:45 PM, swati rana <swati.rana088 at gmail.com>
> > wrote:
> >
> > > Dear Justin,
> > >
> > > Thanks a lot, your suggestions helped me a lot.
> > >
> > > With Regards,
> > > Swati
> > >
> > >
> > > On Sun, Mar 3, 2013 at 1:22 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> > >
> > >>
> > >>
> > >> On 3/2/13 1:42 AM, swati rana wrote:
> > >>
> > >>> Hi Justin,
> > >>>
> > >>> Thanks a lot, that suggestion of yours helped. I am on the
> > >>> equilibration step and its running but nothing is happening on the
> > >>> terminal its just stagnant. Is it fine because its more than 17
> > >>> hrs now. Is there some problem.
> > >>> After running the second command nothing is happening on the
> terminal.
> > >>>
> > >>> grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
> > >>>
> > >>> mdrun -deffnm nvt
> > >>>
> > >>> I am sorry as it is not a reasonable question to ask but i am just
> > >>> asking out of curiosity and lack of time.
> > >>>
> > >>>
> > >> If you're trying to run an MD simulation in serial, you'll get
> > >> terrible performance unless the system is very small (a few hundred
> > >> atoms). Most MD is conducted in parallel on high-performance
> > >> computing clusters, or at the very least on a multi-core
> > >> workstation,
> > again using parallelization.
> > >>
> > >> You won't get constant output in either case, since I/O is buffered
> > >> and write intervals depend on what you specify in the .mdp file.
> > >> In any case, if you're getting poor performance, you're probably
> > >> simply asking your computer to do something it's incapable of
> > >> handling
> > efficiently.
> > >>
> > >>
> > >> -Justin
> > >>
> > >> --
> > >> ==============================**==========
> > >>
> > >> Justin A. Lemkul, Ph.D.
> > >> Research Scientist
> > >> Department of Biochemistry
> > >> Virginia Tech
> > >> Blacksburg, VA
> > >> jalemkul[at]vt.edu | (540) 231-9080
> > >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://w
> > >> ww .bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > >>
> > >> ==============================**==========
> > >> --
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