[gmx-users] Editconf error
Jorge Dagnino
jdagnino at gmail.com
Fri May 22 18:06:12 CEST 2015
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
>
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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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