[gmx-users] Editconf error

Jorge Dagnino jdagnino at gmail.com
Fri May 22 22:57:54 CEST 2015


As this is my first time with this kind of error,  i don't know which part
of the coordinate file is relevant, :(
If you can tell me which part do you need, i  can paste it
Thanks.

2015-05-22 17:17 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 5/22/15 4:07 PM, Jorge Dagnino wrote:
>
>> Here are the complete files.
>>
>> pdb2gmx input: http://pastebin.com/HBmrR0eF
>>
>> .gro output: http://paste2.org/ahY6MB99
>>
>> editconf input: http://paste2.org/9fPp6J02
>>
>> editconf output: http://paste2.org/v1IsPp6O
>>
>>
> Can you just upload all the relevant coordinate files so I don't have to
> copy-paste tens of thousands of lines of text? :)
>
> -Justin
>
>
>  Thanks.
>>
>> 2015-05-22 16:21 GMT-03:00 Barnett, James W <jbarnet4 at tulane.edu>:
>>
>>  It'd be more helpful for troubleshooting your problem if you post the
>>> entire file in each case, not just parts of them. If it's a large file
>>> use
>>> Pastebin.com or something similar.
>>>
>>> --
>>> James "Wes" Barnett
>>> Ph.D. Candidate
>>> Chemical and Biomolecular Engineering
>>>
>>> Tulane University
>>> Boggs Center for Energy and Biotechnology, Room 341-B
>>> New Orleans, Louisiana 70118
>>> jbarnet4 at tulane.edu>>> LinkedIn​​
>>>
>>>
>>> ________________________________________
>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Jorge
>>> Dagnino <jdagnino at gmail.com>
>>> Sent: Friday, May 22, 2015 11:06 AM
>>> To: gmx-users at gromacs.org
>>> Subject: Re: [gmx-users] Editconf error
>>>
>>> Here are the coordinates from my pdb file:
>>>
>>> ATOM      1  N   MET G  27      69.331  43.147  76.443  1.00  0.00
>>>    N
>>> ATOM      2  CA  MET G  27      68.996  44.047  75.331  1.00  0.00
>>>    C
>>> ATOM      3  C   MET G  27      67.818  43.550  74.510  1.00  0.00
>>>    C
>>> ATOM      4  O   MET G  27      66.981  44.264  73.969  1.00  0.00
>>>    O
>>> ATOM      5  CB  MET G  27      70.152  44.201  74.325  1.00  0.00
>>>    C
>>> ATOM      6  CG  MET G  27      70.024  45.547  73.614  1.00  0.00
>>>    C
>>> ATOM      7  SD  MET G  27      70.710  46.841  74.678  1.00  0.00
>>>    S
>>> ATOM      8  CE  MET G  27      70.252  48.118  73.481  1.00  0.00
>>>    C
>>> ATOM      9  N   ALA G  28      67.504  42.250  74.523  1.00  0.00
>>>    N
>>> ATOM     10  CA  ALA G  28      66.247  41.666  74.095  1.00  0.00
>>>    C
>>> ATOM     11  C   ALA G  28      64.968  42.391  74.469  1.00  0.00
>>>    C
>>> ATOM     12  O   ALA G  28      64.064  42.543  73.651  1.00  0.00
>>>    O
>>> ATOM     13  CB  ALA G  28      66.323  40.167  74.396  1.00  0.00
>>>    C
>>> ATOM     14  N   GLU G  29      64.839  42.732  75.756  1.00  0.00
>>>    N
>>> ATOM     15  CA  GLU G  29      63.656  43.315  76.334  1.00  0.00
>>>    C
>>> ATOM     16  C   GLU G  29      63.567  44.789  75.955  1.00  0.00
>>>    C
>>> ATOM     17  O   GLU G  29      62.480  45.354  75.850  1.00  0.00
>>>    O
>>> ATOM     18  CB  GLU G  29      63.662  43.143  77.854  1.00  0.00
>>>    C
>>> ATOM     19  CG  GLU G  29      64.822  43.835  78.553  1.00  0.00
>>>    C
>>> ATOM     20  CD  GLU G  29      64.794  43.644  80.055  1.00  0.00
>>>    C
>>> ATOM     21  OE1 GLU G  29      63.801  44.058  80.689  1.00  0.00
>>>    O
>>> ATOM     22  OE2 GLU G  29      65.765  43.078  80.601  1.00  0.00
>>>    O1-
>>>
>>> And here are the coordinates from the .gro file
>>>
>>> Giant Rising Ordinary Mutants for A Clerical Setup
>>> 16231
>>>     27MET      N    1   6.933   4.315   7.644
>>>     27MET     H1    2   7.011   4.352   7.695
>>>     27MET     H2    3   6.854   4.307   7.705
>>>     27MET     H3    4   6.957   4.224   7.608
>>>     27MET     CA    5   6.900   4.405   7.533
>>>     27MET     HA    6   6.878   4.489   7.582
>>>     27MET     CB    7   7.015   4.420   7.432
>>>     27MET    HB1    8   7.103   4.416   7.481
>>>     27MET    HB2    9   7.011   4.346   7.365
>>>     27MET     CG   10   7.002   4.555   7.361
>>>     27MET    HG1   11   7.052   4.545   7.275
>>>     27MET    HG2   12   6.905   4.567   7.343
>>>     27MET     SD   13   7.071   4.684   7.468
>>>     27MET     CE   14   7.025   4.812   7.348
>>>     27MET    HE1   15   7.053   4.901   7.383
>>>     27MET    HE2   16   7.071   4.794   7.261
>>>     27MET    HE3   17   6.926   4.811   7.334
>>>     27MET      C   18   6.782   4.355   7.451
>>>     27MET      O   19   6.698   4.426   7.397
>>>     28ALA      N   20   6.750   4.225   7.452
>>>     28ALA      H   21   6.820   4.162   7.486
>>>     28ALA     CA   22   6.625   4.167   7.410
>>>     28ALA     HA   23   6.620   4.184   7.311
>>>     28ALA     CB   24   6.632   4.017   7.440
>>>     28ALA    HB1   25   6.547   3.973   7.411
>>>     28ALA    HB2   26   6.709   3.976   7.389
>>>     28ALA    HB3   27   6.646   4.003   7.538
>>>     28ALA      C   28   6.497   4.239   7.447
>>>     28ALA      O   29   6.406   4.254   7.365
>>>     29GLU      N   30   6.484   4.273   7.576
>>>     29GLU      H   31   6.562   4.257   7.636
>>>     29GLU     CA   32   6.366   4.332   7.633
>>>     29GLU     HA   33   6.289   4.281   7.594
>>>     29GLU     CB   34   6.366   4.314   7.785
>>>     29GLU    HB1   35   6.281   4.352   7.822
>>>     29GLU    HB2   36   6.371   4.217   7.806
>>>     29GLU     CG   37   6.482   4.384   7.855
>>>     29GLU    HG1   38   6.568   4.346   7.820
>>>     29GLU    HG2   39   6.478   4.481   7.836
>>>     29GLU     CD   40   6.479   4.364   8.005
>>>     29GLU    OE1   41   6.380   4.406   8.069
>>>     29GLU    OE2   42   6.576   4.308   8.060
>>>     29GLU      C   43   6.357   4.479   7.595
>>>     29GLU      O   44   6.248   4.535   7.585
>>>
>>> and this is the output from editconf.
>>>
>>> Giant Rising Ordinary Mutants for A Clerical Setup
>>> 16231
>>>     27MET      N    1    -nan    -nan    -nan
>>>     27MET     H1    2    -nan    -nan    -nan
>>>     27MET     H2    3    -nan    -nan    -nan
>>>     27MET     H3    4    -nan    -nan    -nan
>>>     27MET     CA    5    -nan    -nan    -nan
>>>     27MET     HA    6    -nan    -nan    -nan
>>>     27MET     CB    7    -nan    -nan    -nan
>>>     27MET    HB1    8    -nan    -nan    -nan
>>>     27MET    HB2    9    -nan    -nan    -nan
>>>     27MET     CG   10    -nan    -nan    -nan
>>>     27MET    HG1   11    -nan    -nan    -nan
>>>     27MET    HG2   12    -nan    -nan    -nan
>>>     27MET     SD   13    -nan    -nan    -nan
>>>     27MET     CE   14    -nan    -nan    -nan
>>>     27MET    HE1   15    -nan    -nan    -nan
>>>     27MET    HE2   16    -nan    -nan    -nan
>>>     27MET    HE3   17    -nan    -nan    -nan
>>>     27MET      C   18    -nan    -nan    -nan
>>>     27MET      O   19    -nan    -nan    -nan
>>>
>>> I hope that this helps.
>>> Thanks
>>>
>>>
>>> 2015-05-20 22:28 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:
>>>
>>>
>>>>
>>>> On 5/20/15 5:27 PM, Jorge Dagnino wrote:
>>>>
>>>>  Dear GMX users.
>>>>>
>>>>> Im trying to create my system and When i use pdb2gmx everything seems
>>>>>
>>>> ok.
>>>
>>>>
>>>>> gmx pdb2gmx -f trim.pdb -o trim.gro -water spce -chainsep id
>>>>>
>>>>> Including chain 1 in system: 3235 atoms 203 residues
>>>>> Including chain 2 in system: 2531 atoms 161 residues
>>>>> Including chain 3 in system: 2546 atoms 161 residues
>>>>> Including chain 4 in system: 2531 atoms 161 residues
>>>>> Including chain 5 in system: 2546 atoms 161 residues
>>>>> Including chain 6 in system: 2842 atoms 169 residues
>>>>> Now there are 16231 atoms and 1016 residues
>>>>> Total mass in system 115288.734 a.m.u.
>>>>> Total charge in system -17.000 e
>>>>>
>>>>> Writing coordinate file...
>>>>>
>>>>> --------- PLEASE NOTE ------------
>>>>> You have successfully generated a topology from: trim.pdb.
>>>>> The OplsaaPBS force field and the spce water model are used.
>>>>>
>>>>> Then when i use the editconf command :
>>>>>
>>>>> gmx editconf -f trim.gro -bt dodecahedron -o box -c -d 1.0
>>>>>
>>>>>
>>>>> Read 16231 atoms
>>>>> Volume: 60.3503 nm^3, corresponds to roughly 27100 electrons
>>>>> No velocities found
>>>>>       system size : 11.777 11.005  6.369 (nm)
>>>>>       diameter    : 12.737               (nm)
>>>>>       center      :   -nan   -nan   -nan (nm)
>>>>>       box vectors :  4.144  4.582  3.178 (nm)
>>>>>       box angles  :  90.00  90.00  90.00 (degrees)
>>>>>       box volume  :  60.35               (nm^3)
>>>>>       shift       :   -nan   -nan   -nan (nm)
>>>>> new center      :   -nan   -nan   -nan (nm)
>>>>> new box vectors : 14.737 14.737 14.737 (nm)
>>>>> new box angles  :  60.00  60.00  90.00 (degrees)
>>>>> new box volume  :2262.99               (nm^3)
>>>>>
>>>>> and the ouptut file looks like this.
>>>>>
>>>>> Giant Rising Ordinary Mutants for A Clerical Setup
>>>>> 16231
>>>>>      27MET      N    1    -nan    -nan    -nan
>>>>>      27MET     H1    2    -nan    -nan    -nan
>>>>>      27MET     H2    3    -nan    -nan    -nan
>>>>>      27MET     H3    4    -nan    -nan    -nan
>>>>>      27MET     CA    5    -nan    -nan    -nan
>>>>>
>>>>> I try to make a bigger box manually, also change the box shape and the
>>>>> distance but i have the same result,
>>>>> This is my first time with this kind of error, what is wrong? what am i
>>>>> missing?
>>>>>
>>>>>
>>>> Hard to say; I've never seen anything like this.  The 'nan' means "not a
>>>> number" so the coordinates are junk.  Are the coordinates in trim.pdb
>>>> and
>>>> trim.gro sound?
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 629
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
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>>>> posting!
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>>>>
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>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>>>
>>>
>>> --
>>> JORGE DAGNINO LEONE
>>> Bioquímico
>>> Magíster en Bioquímica y Bioinformática
>>> Estudiante de Doctorado en Ciencias Biológicas.
>>> Facultad de Ciencias Biológicas
>>> Laboratorio de Biofísica Molecular
>>> Universidad de Concepción
>>> --
>>> Gromacs Users mailing list
>>>
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>>> posting!
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>>>
>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
JORGE DAGNINO LEONE
Bioquímico
Magíster en Bioquímica y Bioinformática
Estudiante de Doctorado en Ciencias Biológicas.
Facultad de Ciencias Biológicas
Laboratorio de Biofísica Molecular
Universidad de Concepción


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