[gmx-users] about the topology file
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Nov 2 13:02:43 CET 2006
Hi Xiangyang Liu,
You have to check the lines in the top files which are indicated by
the warnings. It seems something goes wrong there, or maybe elsewhere
still, which screws up the top file, making grompp "think" that it
hasn't read any atoms there at all. Just recently the same issue was
reported on the user list, which was caused by an #ifdef statement,
which wasn't closed with #end.
Note, if I understand well, you're using a prodrg created topology. I
believe these are still based on the ffgmx force field, the old gromos
87 force field, which is deprecated and shouldn't be used for
production runs. You have to try to convert your topology to a newer
gromos force field.
Best,
Tsjerk
On 11/2/06, Xiangyang Liu <shangdongliu at gmail.com> wrote:
> hello Tsjerk:
> Thank you very much! That does work, but another problem appeared as
> following:
> creating statusfile for 1 node...
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 1284 of the 1485 non-bonded parameter combinations
> WARNING 1 [file " com.top", line 519]:
> Too few parameters on line (source file toppush.c, line 932)
> WARNING 2 [file "com.top", line 520]:
> Too few parameters on line (source file toppush.c, line 932)
> processing coordinates...
> Fatal error: number of coordinates in coordinate file (com_wat.gro, 2837)
> does not match topology (com.top, 0)
> actually i only perform the following:
>
>
> editconf –bt cubic –f com.gro –o com_box.gro –d 0.8
>
> genbox –cp com_box.gro –cs spc216.gro –p com.top –o com_wat.gro
>
> grompp –f em.mdp –c com_wat.gro –p com.top –o com_em.tpr
>
> and my com.gro file was as following:
>
> PRODRG COORDS
> 80
> 1DRG CAH 1 -0.832 -0.624 -0.960
> 1DRG CAS 2 -0.746 -0.538 -0.867
> 1DRG CAT 3 -0.710 -0.410 - 0.942
> 1DRG CBI 4 -0.621 -0.618 -0.830
> 1DRG CCF 5 -0.555 -0.585 -0.694
> 1DRG CCG 6 -0.647 -0.615 -0.575
> 1DRG OCU 7 -0.750 -0.706 -0.587
> 1DRG OBJ 8 - 0.629 -0.560 -0.467
> 1DRG NCE 9 -0.506 -0.445 -0.688
> 1DRG HAG 10 -0.556 -0.385 -0.626
> 1DRG CCD 11 -0.401 -0.405 -0.761
> 1DRG OBH 12 -0.345 -0.480 -0.843
> 1DRG CCC 13 - 0.347 -0.263 -0.745
> 1DRG CBG 14 -0.439 -0.163 -0.817
> 1DRG CAQ 15 -0.381 -0.024 -0.851
> 1DRG CAG 16 -0.248 -0.030 -0.926
> 1DRG CAR 17 -0.363 0.065 -0.727
> 1DRG NCB 18 - 0.326 -0.229 -0.603
> 1DRG HAF 19 -0.405 -0.241 -0.543
> 1DRG CCA 20 -0.206 -0.185 -0.563
> 1DRG OBF 21 -0.113 -0.159 -0.640
> 1DRG CBZ 22 -0.187 -0.168 -0.413
> 1DRG CBE 23 - 0.126 -0.302 -0.370
> 1DRG CAO 24 -0.241 -0.394 -0.332
> 1DRG OAF 25 -0.338 -0.339 -0.274
> 1DRG OAP 26 -0.230 -0.514 -0.360
> 1DRG NBY 27 -0.106 -0.046 -0.388
> 1DRG HAE 28 - 0.084 0.000 -0.473
> 1DRG CBX 29 -0.062 0.009 -0.273
> 1DRG OBD 30 -0.012 0.122 -0.272
> 1DRG CBW 31 -0.067 -0.063 -0.137
> 1DRG CBC 32 0.078 -0.071 -0.084
> 1DRG CAN 33 0.164 -0.170 -0.163
> 1DRG CBB 34 0.089 -0.114 0.063
> 1DRG NBV 35 -0.154 0.013 -0.045
> 1DRG HAD 36 -0.131 0.111 -0.043
> 1DRG CBU 37 -0.254 -0.032 0.032
> 1DRG OBA 38 - 0.296 0.039 0.123
> 1DRG CBT 39 -0.315 -0.174 0.014
> 1DRG CAZ 40 -0.241 -0.277 0.099
> 1DRG CAL 41 -0.206 -0.403 0.018
> 1DRG CAE 42 -0.326 -0.495 -0.002
> 1DRG CAM 43 - 0.094 -0.481 0.088
> 1DRG NBS 44 -0.452 -0.166 0.069
> 1DRG HAC 45 -0.449 -0.181 0.167
> 1DRG CBR 46 -0.575 -0.144 0.017
> 1DRG OAY 47 -0.666 -0.135 0.100
> 1DRG CBQ 48 - 0.618 -0.126 -0.131
> 1DRG CAX 49 -0.520 -0.056 -0.228
> 1DRG CAJ 50 -0.533 0.096 -0.242
> 1DRG CAD 51 -0.499 0.173 -0.114
> 1DRG CAK 52 -0.673 0.137 -0.289
> 1DRG NBP 53 - 0.666 -0.245 -0.201
> 1DRG HAB 54 -0.595 -0.302 -0.244
> 1DRG C 55 -0.797 -0.274 -0.207
> 1DRG O 56 -0.872 -0.267 -0.109
> 1DRG CA 57 -0.856 -0.322 -0.340
> 1DRG CB 58 - 0.777 -0.276 -0.463
> 1DRG CG 59 -0.821 -0.140 -0.516
> 1DRG CD 60 -0.725 -0.105 -0.629
> 1DRG OE2 61 -0.635 -0.023 -0.602
> 1DRG OE1 62 -0.741 -0.164 -0.738
> 1DRG N 63 - 0.871 -0.467 -0.358
> 1DRG HAA 64 -0.795 -0.522 -0.325
> 1DRG CBL 65 -0.981 -0.519 -0.414
> 1DRG OAU 66 -1.093 -0.467 -0.410
> 1DRG CBK 67 -0.968 -0.654 -0.484
> 1DRG CCT 68 - 0.833 -0.725 -0.469
> 1DRG CCS 69 -0.860 -0.875 -0.449
> 1DRG CCR 70 -0.929 -0.913 -0.316
> 1DRG CCQ 71 -0.842 -0.888 -0.192
> 1DRG CCP 72 -0.880 -0.760 -0.116
> 1DRG CCO 73 - 0.763 -0.714 -0.029
> 1DRG CCN 74 -0.792 -0.577 0.034
> 1DRG CCM 75 -0.676 -0.523 0.119
> 1DRG CCL 76 -0.670 -0.578 0.263
> 1DRG CCK 77 -0.593 -0.710 0.282
> 1DRG CCJ 78 - 0.440 -0.698 0.279
> 1DRG CCI 79 -0.385 -0.625 0.402
> 1DRG CCH 80 -0.232 -0.622 0.401
> 1.51200 1.51200 1.51200
> Thank you very much!
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--
Tsjerk A. Wassenaar, Ph.D.
post-doc
NMR, Utrecht University,
Padualaan 8,
3584 CH Utrecht, the Netherlands
P: +31-30-2539931
F: +31-30-2537623
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