<font size="-1">Hi <br>
<br>
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.<br>
<br>
Gaurav<br>
<br>
</font>
<div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><font size="-1">Gaurav Chopra wrote:<br>> Hi<br>><br>> I am getting the following error with mdrun. I have done a few things
<br>> but the system complains of 1-4 interactions and gives LINCS warning if<br>> the constraints are not turned off in the mdp file. I also changed the<br>> fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I
<br>> get 1-4 interaction table size error and then LINCS warning. The output<br>> of mdrun for one of these peptides is as follows. I am working on normal<br>> mode decoys of each peptide and many of the decoys have no problems with
<br>> mdrun but some gives this error and Segmentation Fault.<br>><br>> Please advice.<br>><br>><br>you need to minimize better, but if your structures are really bad it<br>won't help either (e.g. when you have a sidechain sticking through a ring)
<br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.
<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">spoel@gromacs.org
</a> <a href="http://folding.bmc.uu.se/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>
<br><br>The lincs warnning are on water molecules isn't it ???<br><br>XAvier
<br><br><br>
</font></blockquote></div>
<font size="-1">Output set 710 with rmsf= 1.614 of 1dsl.cl_nH_tir.pdb in water</font><br>
<font size="-1"><br>
49GLU HB2 797 4.183 3.686 4.460<br>
49GLU CG 798 4.026 3.813 4.538<br>
49GLU HG1 799 4.042 3.915 4.502<br>
49GLU HG2 800 3.919 3.800 4.550<br>
49GLU CD 801 4.094 3.805 4.672<br>
49GLU OE1 802 4.149 3.697 4.707<br>
49GLU OE2 803 4.086 3.910 4.737<br>
49GLU C 804 4.170 3.865 4.250<br>
49GLU O 805 4.144 3.984 4.263<br>
50MET N 806 4.286 3.822 4.199<br>
50MET H 807 4.301 3.722 4.190<br>
50MET CA 808 4.405 3.904 4.182<br>
50MET HA 809 4.377 4.008 4.198<br>
50MET CB 810 4.510 3.865 4.285<br>
50MET HB1 811 4.565 3.777 4.252<br>
50MET HB2 812 4.587 3.940 4.292<br>
50MET CG 813 4.452 3.835 4.423<br>
50MET HG1 814 4.353 3.796 4.425<br>
50MET HG2 815 4.514 3.755 4.462<br>
50MET SD 816 4.453 3.976 4.531<br>
50MET CE 817 4.614 3.925 4.588<br>
50MET HE1 818 4.659 3.996 4.655<br>
50MET HE2 819 4.599 3.831 4.640<br>
50MET HE3 820 4.679 3.909 4.502<br>
50MET C 821 4.467 3.887 4.044<br>
50MET O 822 4.445 3.784 3.981<br>
51PRO N 823 4.549 3.984 4.000<br>
51PRO CA 824 4.626 3.972 3.876<br>
51PRO HA 825 4.553 3.969 3.796<br>
51PRO CB 826 4.711 4.099 3.867<br>
51PRO HB1 827 4.810 4.080 3.908<br>
51PRO HB2 828 4.721 4.135 3.765<br>
51PRO CG 829 4.639 4.199 3.954<br>
51PRO HG1 830 4.708 4.273 3.991<br>
51PRO HG2 831 4.564 4.251 3.895<br>
51PRO CD 832 4.572 4.115 4.061<br>
51PRO HD1 833 4.644 4.098 4.141<br>
51PRO HD2 834 4.483 4.163 4.101<br>
51PRO C 835 4.718 3.850 3.874<br>
51PRO O 836 4.762 3.800 3.978<br>
52SER N 837 4.744 3.801 3.753<br>
52SER H 838 4.711 3.859 3.675<br>
52SER CA 839 4.833 3.689 3.720<br>
52SER HA 840 4.822 3.669 3.614<br>
52SER CB 841 4.978 3.722 3.756<br>
52SER HB1 842 4.988 3.744 3.862<br>
52SER HB2 843 5.041 3.636 3.736<br>
52SER OG 844 5.030 3.825 3.676<br>
52SER HG 845 5.110 3.854 3.717<br>
52SER C 846 4.797 3.559 3.791<br>
52SER O 847 4.884 3.479 3.827<br>
53TYR N 848 4.667 3.537 3.811<br>
53TYR H 849 4.602 3.601 3.770<br>
53TYR CA 850 4.613 3.409 3.852<br>
53TYR HA 851 4.505 3.420 3.851<br>
53TYR CB 852 4.645 3.304 3.741<br>
53TYR HB1 853 4.747 3.275 3.756<br>
53TYR HB2 854 4.589 3.212 3.749<br>
53TYR CG 855 4.643 3.353 3.597<br>
53TYR CD1 856 4.529 3.414 3.540<br>
53TYR HD1 857 4.437 3.421 3.595<br>
53TYR CD2 858 4.764 3.349 3.524<br>
53TYR HD2 859 4.854 3.308 3.568<br>
53TYR CE1 860 4.537 3.471 3.411<br>
53TYR HE1 861 4.452 3.523 3.370<br>
53TYR CE2 862 4.770 3.401 3.394<br>
53TYR HE2 863 4.862 3.395 3.338<br>
53TYR CZ 864 4.656 3.460 3.337<br>
53TYR OH 865 4.662 3.504 3.209<br>
53TYR HH 866 4.747 3.489 3.170<br>
53TYR C 867 4.657 3.374 4.000<br>
53TYR O 868 4.670 3.255 4.028<br>
54ARG N 869 4.682 3.473 4.093<br>
54ARG H 870 4.661 3.565 4.055<br>
54ARG CA 871 4.673 3.444 4.245<br>
54ARG HA 872 4.700 3.339 4.251<br>
54ARG CB 873 4.754 3.510 4.374<br>
54ARG HB1 874 4.855 3.504 4.327<br>
54ARG HB2 875 4.748 3.618 4.351<br>
54ARG CG 876 4.730 3.461 4.557<br>
54ARG HG1 877 4.799 3.379 4.533<br>
54ARG HG2 878 4.812 3.521 4.599<br>
54ARG CD 879 4.604 3.380 4.698<br>
54ARG HD1 880 4.559 3.315 4.625<br>
54ARG HD2 881 4.667 3.298 4.735<br>
54ARG NE 882 4.459 3.405 4.816<br>
54ARG HE 883 4.508 3.338 4.886<br>
54ARG CZ 884 4.385 3.397 4.953<br>
54ARG NH1 885 4.342 3.454 4.851<br>
54ARG HH11 886 4.441 3.411 4.820<br>
54ARG HH12 887 4.246 3.444 4.821<br>
54ARG NH2 888 4.261 3.401 5.023<br>
54ARG HH21 889 4.246 3.370 5.123<br>
54ARG HH22 890 4.176 3.464 5.021<br>
54ARG C 891 4.534 3.490 4.285<br>
54ARG O 892 4.460 3.564 4.222<br>
55GLY N 893 4.517 3.462 4.410<br>
55GLY H 894 4.605 3.428 4.447<br>
55GLY CA 895 4.425 3.510 4.506<br>
55GLY HA1 896 4.471 3.539 4.600<br>
55GLY HA2 897 4.375 3.599 4.478<br>
55GLY C 898 4.336 3.393 4.525<br>
55GLY O 899 4.363 3.279 4.483<br>
56ARG N 900 4.226 3.424 4.591<br>
56ARG H 901 4.219 3.519 4.627</font>