[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
Thu Mar 21 07:09:24 CET 2013
Hi,
Thanks Emanuel the problem is resolved by changing the atom name in spc.itp
file but question is can we do it. Will it be fine or will it create some
problems in the future process. I changed OW to OW1 in spc file.
With Regards,
Swati
On Thu, Mar 21, 2013 at 11:30 AM, swati rana <swati.rana088 at gmail.com>wrote:
> 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://www
>> >> .bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >>
>> >> ==============================**==========
>> >> --
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