[gmx-users] RE: gro file and topology files
Justin A. Lemkul
jalemkul at vt.edu
Tue Nov 9 19:37:26 CET 2010
Nimesh Jain wrote:
> Hi,
>
> I was wondering if the order of molecules in topology file and the order
> of coordinates in gro file have to be same. My files are as follows:
>
> gro file:
> 1624
> 1B1 C 1 22.237 30.408 26.522
> 1B1 SA 2 22.348 30.033 26.829
> 1B1 P 3 22.125 30.102 27.144
> 2B2 T 4 21.852 30.069 26.468
> 2B2 SA 5 21.824 30.189 26.949
> 2B2 P 6 21.450 30.060 27.068
> 3B3 G 7 21.778 29.762 26.361
> 3B3 SA 8 21.321 30.008 26.724
> 3B3 P 9 20.949 29.853 26.660
> 4B4 G 10 21.629 29.470 26.321
> 4B4 SA 11 21.026 29.716 26.325
> 4B4 P 12 20.750 29.499 26.117
> 5B5 A 13 21.487 29.154 26.338
> 5B5 SA 14 20.990 29.299 25.943
> 5B5 P 15 20.872 28.995 25.697
> 6B6 G 16 21.351 28.838 26.366
> 6B6 SA 17 21.165 28.798 25.747
> 6B6 P 18 21.201 28.428 25.579
> 7B7 A 19 21.229 28.513 26.410
> 7B7 SA 20 21.416 28.303 25.825
> 7B7 P 21 21.542 27.915 25.815
> 8B8 T 22 21.195 28.076 26.416
> 8B8 SA 23 21.574 27.883 26.158
> 8B8 P 24 21.640 27.516 26.330
> 9B9 A 25 20.912 27.888 26.523
> 9B9 SA 26 21.488 27.595 26.632
> ...................................................
> ................................................... upto 880
> particles then,
> 295NEU NEU 881 27.530 28.268 24.349
> 296NEU NEU 882 27.355 27.969 24.193
> 297NEU NEU 883 27.623 27.876 23.941
> 298NEU NEU 884 27.801 27.639 24.177
> 299NEU NEU 885 27.473 27.507 24.322
> 300NEU NEU 886 27.376 27.410 23.963
> 301NEU NEU 887 27.316 26.930 24.121
> 302NEU NEU 888 27.540 26.452 24.221
> 303NEU NEU 889 27.266 26.353 23.979
> 304NEU NEU 890 27.681 25.977 24.053
> 305NEU NEU 891 27.538 25.708 24.281
> ............................................................. upto 1416
> particles then,
> 831POS POS 1417 27.764 28.400 24.075
> 832POS POS 1418 27.717 27.250 23.909
> 833POS POS 1419 27.466 26.805 23.792
> 834POS POS 1420 27.758 26.635 23.970
> 835POS POS 1421 27.530 26.183 23.770
> 836POS POS 1422 27.930 25.982 25.593
> 837POS POS 1423 27.940 25.614 25.687
> 838POS POS 1424 27.629 25.568 26.499
> 839POS POS 1425 27.293 25.195 26.653
> 840POS POS 1426 26.656 24.646 27.207
> 841POS POS 1427 27.493 24.378 26.671
> 842POS POS 1428 25.704 28.084 24.322
> 843POS POS 1429 26.024 28.033 24.522
> 844POS POS 1430 25.690 27.436 25.511
> 845POS POS 1431 25.499 26.486 25.378
> ............................................................... upto
> 1553 particles then,
> 968NEG NEG 1554 27.665 27.041 24.226
> 969NEG NEG 1555 27.770 25.717 24.582
> 970NEG NEG 1556 27.165 25.469 26.884
> 971NEG NEG 1557 26.602 25.231 27.215
> 972NEG NEG 1558 27.309 24.502 27.300
> 973NEG NEG 1559 27.075 25.317 25.083
> 974NEG NEG 1560 26.927 25.837 25.127
> 975NEG NEG 1561 26.247 26.641 24.480
> 976NEG NEG 1562 25.888 26.676 24.614
> 977NEG NEG 1563 25.773 27.276 25.174
> 978NEG NEG 1564 25.345 26.065 25.614
> 979NEG NEG 1565 24.862 26.307 25.737
> 980NEG NEG 1566 27.642 26.470 26.780
> 981NEG NEG 1567 26.721 27.065 26.145
> 982NEG NEG 1568 26.398 26.984 25.969
> 983NEG NEG 1569 26.291 25.493 26.397
> 984NEG NEG 1570 26.029 24.681 26.249
> 985NEG NEG 1571 26.374 23.945 26.814
> 986NEG NEG 1572 26.551 24.207 25.873
> 987NEG NEG 1573 27.184 23.760 24.934
> 988NEG NEG 1574 25.102 22.440 25.649
> 989NEG NEG 1575 23.763 24.119 26.999
> ..........................1624 particles ...
>
>
>
> topology
> ...........................................
> ...................................
> [ moleculetype ]
> Neutral 1
>
> [ atoms ]
> 1 NEU 1 NEU NEU 1
>
> [ moleculetype ]
> Positive 1
>
> [ atoms ]
> 1 POS 1 POS POS 1
>
> [ moleculetype ]
> Negative 1
>
> [ atoms ]
> 1 NEG 1 NEG NEG 1
>
> [ moleculetype ]
> SS1 1
>
> [ atoms ]
> 1 C 1 B1 C 1
> 2 SA 1 S1 SA 2
> 3 P 1 P1 P 3
> 4 T 2 B2 T 4
> 5 SA 2 S2 SA 5
> 6 P 2 P2 P 6
> 7 G 3 B3 G 7
> 8 SA 3 S3 SA 8
> 9 P 3 P3 P 9
> 10 G 4 B4 G 10
> 11 SA 4 S4 SA 11
> 12 P 4 P4 P 12
> 13 A 5 B5 A 13
> 14 SA 5 S5 SA 14
>
> The starting coordinates in gro file belong to molecule SS1 in topology
> file. As you can see, the coordinates for NEU, POS and NEG particles are
> towards the end in gro file but I am defining these particles in the
> beginning of topology file. Please let me know if this is ok or is it
> wrong ? And how can I check.
>
The only order that is pertinent is that of the [molecules] directive in the
.top file. It must match that of the coordinate file. If not, grompp will exit
with a fatal error. That's a fairly obvious way to check :)
-Justin
> Thanks,
> Nimesh
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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