<pre>Hi<br><br>Attached is part of the gro file which gave the LINCS error on atoms. This<br>output is the gro file for the initial mdrun, after which final grompp and<br>final mdrun was done, which gives the error I described in the message
<br>below.<br><br>Gaurav<br><br> Gaurav Chopra wrote:<br>><i> > Hi<br></i>><i> ><br></i>><i> > I am getting the following error with mdrun. I have done a few things<br></i>><i> > but the system complains of 1-4 interactions and gives LINCS warning if
<br></i>><i> > the constraints are not turned off in the mdp file. I also changed the<br></i>><i> > fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I<br></i>><i> > get 1-4 interaction table size error and then LINCS warning. The output
<br></i>><i> > of mdrun for one of these peptides is as follows. I am working on normal<br></i>><i> > mode decoys of each peptide and many of the decoys have no problems with<br></i>><i><br></i>><i> > mdrun but some gives this error and Segmentation Fault.
<br></i>><i> ><br></i>><i> > Please advice.<br></i>><i> ><br></i>><i> ><br></i>><i> you need to minimize better, but if your structures are really bad it<br></i>><i> won't help either (e.g. when you have a sidechain sticking through a ring)
<br></i>><i><br></i>><i><br></i>><i> --<br></i>><i> David.<br></i>><i> ________________________________________________________________________<br></i>><i> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
<br></i>><i> Dept. of Cell and Molecular Biology, Uppsala University.<br></i>><i> Husargatan 3, Box 596, 75124 Uppsala, Sweden<br></i>><i> phone: 46 18 471 4205 fax: 46 18 511 755<br></i>><i>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users">spoel at xray.bmc.uu.se</a> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">spoel at gromacs.org</a> <a href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se
</a><br></i>><i> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br></i>><i><br></i>><i><br></i>><i> The lincs warnning are on water molecules isn't it ???<br></i>><i><br></i>><i>
XAvier<br></i>><i><br></i>><i><br></i>><i> Output set 710 with rmsf= 1.614 of 1dsl.cl_nH_tir.pdb in water<br></i><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</pre>