[gmx-users] LINCS Warning with MDRUN - Segmentation Fault
Gaurav Chopra
gauravchopra at gmail.com
Thu Apr 20 03:00:23 CEST 2006
Hi
Attached is part of the gro file which gave the LINCS error on atoms. This
output is the gro file for the initial mdrun, after which final grompp and
final mdrun was done, which gives the error I described in the message
below.
Gaurav
Gaurav Chopra wrote:
>* > Hi
*>* >
*>* > I am getting the following error with mdrun. I have done a few things
*>* > but the system complains of 1-4 interactions and gives LINCS warning if
*>* > the constraints are not turned off in the mdp file. I also changed the
*>* > fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I
*>* > get 1-4 interaction table size error and then LINCS warning. The output
*>* > of mdrun for one of these peptides is as follows. I am working on normal
*>* > mode decoys of each peptide and many of the decoys have no problems with
*>*
*>* > mdrun but some gives this error and Segmentation Fault.
*>* >
*>* > Please advice.
*>* >
*>* >
*>* you need to minimize better, but if your structures are really bad it
*>* won't help either (e.g. when you have a sidechain sticking through a ring)
*>*
*>*
*>* --
*>* David.
*>* ________________________________________________________________________
*>* David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
*>* Dept. of Cell and Molecular Biology, Uppsala University.
*>* Husargatan 3, Box 596, 75124 Uppsala, Sweden
*>* phone: 46 18 471 4205 fax: 46 18 511 755
*>* spoel at xray.bmc.uu.se
<http://www.gromacs.org/mailman/listinfo/gmx-users> spoel at
gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users>
http://folding.bmc.uu.se
*>* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
*>*
*>*
*>* The lincs warnning are on water molecules isn't it ???
*>*
*>* XAvier
*>*
*>*
*>* Output set 710 with rmsf= 1.614 of 1dsl.cl_nH_tir.pdb in water
*
49GLU HB2 797 4.183 3.686 4.460
49GLU CG 798 4.026 3.813 4.538
49GLU HG1 799 4.042 3.915 4.502
49GLU HG2 800 3.919 3.800 4.550
49GLU CD 801 4.094 3.805 4.672
49GLU OE1 802 4.149 3.697 4.707
49GLU OE2 803 4.086 3.910 4.737
49GLU C 804 4.170 3.865 4.250
49GLU O 805 4.144 3.984 4.263
50MET N 806 4.286 3.822 4.199
50MET H 807 4.301 3.722 4.190
50MET CA 808 4.405 3.904 4.182
50MET HA 809 4.377 4.008 4.198
50MET CB 810 4.510 3.865 4.285
50MET HB1 811 4.565 3.777 4.252
50MET HB2 812 4.587 3.940 4.292
50MET CG 813 4.452 3.835 4.423
50MET HG1 814 4.353 3.796 4.425
50MET HG2 815 4.514 3.755 4.462
50MET SD 816 4.453 3.976 4.531
50MET CE 817 4.614 3.925 4.588
50MET HE1 818 4.659 3.996 4.655
50MET HE2 819 4.599 3.831 4.640
50MET HE3 820 4.679 3.909 4.502
50MET C 821 4.467 3.887 4.044
50MET O 822 4.445 3.784 3.981
51PRO N 823 4.549 3.984 4.000
51PRO CA 824 4.626 3.972 3.876
51PRO HA 825 4.553 3.969 3.796
51PRO CB 826 4.711 4.099 3.867
51PRO HB1 827 4.810 4.080 3.908
51PRO HB2 828 4.721 4.135 3.765
51PRO CG 829 4.639 4.199 3.954
51PRO HG1 830 4.708 4.273 3.991
51PRO HG2 831 4.564 4.251 3.895
51PRO CD 832 4.572 4.115 4.061
51PRO HD1 833 4.644 4.098 4.141
51PRO HD2 834 4.483 4.163 4.101
51PRO C 835 4.718 3.850 3.874
51PRO O 836 4.762 3.800 3.978
52SER N 837 4.744 3.801 3.753
52SER H 838 4.711 3.859 3.675
52SER CA 839 4.833 3.689 3.720
52SER HA 840 4.822 3.669 3.614
52SER CB 841 4.978 3.722 3.756
52SER HB1 842 4.988 3.744 3.862
52SER HB2 843 5.041 3.636 3.736
52SER OG 844 5.030 3.825 3.676
52SER HG 845 5.110 3.854 3.717
52SER C 846 4.797 3.559 3.791
52SER O 847 4.884 3.479 3.827
53TYR N 848 4.667 3.537 3.811
53TYR H 849 4.602 3.601 3.770
53TYR CA 850 4.613 3.409 3.852
53TYR HA 851 4.505 3.420 3.851
53TYR CB 852 4.645 3.304 3.741
53TYR HB1 853 4.747 3.275 3.756
53TYR HB2 854 4.589 3.212 3.749
53TYR CG 855 4.643 3.353 3.597
53TYR CD1 856 4.529 3.414 3.540
53TYR HD1 857 4.437 3.421 3.595
53TYR CD2 858 4.764 3.349 3.524
53TYR HD2 859 4.854 3.308 3.568
53TYR CE1 860 4.537 3.471 3.411
53TYR HE1 861 4.452 3.523 3.370
53TYR CE2 862 4.770 3.401 3.394
53TYR HE2 863 4.862 3.395 3.338
53TYR CZ 864 4.656 3.460 3.337
53TYR OH 865 4.662 3.504 3.209
53TYR HH 866 4.747 3.489 3.170
53TYR C 867 4.657 3.374 4.000
53TYR O 868 4.670 3.255 4.028
54ARG N 869 4.682 3.473 4.093
54ARG H 870 4.661 3.565 4.055
54ARG CA 871 4.673 3.444 4.245
54ARG HA 872 4.700 3.339 4.251
54ARG CB 873 4.754 3.510 4.374
54ARG HB1 874 4.855 3.504 4.327
54ARG HB2 875 4.748 3.618 4.351
54ARG CG 876 4.730 3.461 4.557
54ARG HG1 877 4.799 3.379 4.533
54ARG HG2 878 4.812 3.521 4.599
54ARG CD 879 4.604 3.380 4.698
54ARG HD1 880 4.559 3.315 4.625
54ARG HD2 881 4.667 3.298 4.735
54ARG NE 882 4.459 3.405 4.816
54ARG HE 883 4.508 3.338 4.886
54ARG CZ 884 4.385 3.397 4.953
54ARG NH1 885 4.342 3.454 4.851
54ARG HH11 886 4.441 3.411 4.820
54ARG HH12 887 4.246 3.444 4.821
54ARG NH2 888 4.261 3.401 5.023
54ARG HH21 889 4.246 3.370 5.123
54ARG HH22 890 4.176 3.464 5.021
54ARG C 891 4.534 3.490 4.285
54ARG O 892 4.460 3.564 4.222
55GLY N 893 4.517 3.462 4.410
55GLY H 894 4.605 3.428 4.447
55GLY CA 895 4.425 3.510 4.506
55GLY HA1 896 4.471 3.539 4.600
55GLY HA2 897 4.375 3.599 4.478
55GLY C 898 4.336 3.393 4.525
55GLY O 899 4.363 3.279 4.483
56ARG N 900 4.226 3.424 4.591
56ARG H 901 4.219 3.519 4.627
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