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 <[EMAIL PROTECTED]> 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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