[gmx-users] about the topology file
Moore, Jonathan (J)
JMoore2 at dow.com
Thu Nov 2 14:16:29 CET 2006
See the following from the archive for a possible source of the "number of coordinates...does not match" error.
http://www.gromacs.org/pipermail/gmx-users/2006-October/024223.html <http://www.gromacs.org/pipermail/gmx-users/2006-October/024223.html>
Thanks,
Jonathan
____________________________
Jonathan Moore, Ph.D.
Research and Engineering Sciences - New Products
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The Dow Chemical Company
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-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Xiangyang Liu
Sent: Thursday, November 02, 2006 6:32 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] about the topology file
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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