[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
>>>>
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>>>>
>>>>
>>>
>>>
>>> --
>>> 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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>>
>>
>>
> --
> ==================================================
>
> 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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>
--
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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