[gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093)
Emanuel Birru
Emanuel.Birru at monash.edu
Thu Mar 21 07:11:33 CET 2013
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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