[gmx-users] Editconf error
Justin Lemkul
jalemkul at vt.edu
Fri May 22 22:18:08 CEST 2015
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
==================================================
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