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AMBER Archive (2004)
Subject: AMBER: installation test question (antechamber, ash)
From: Charles F. Fisher (chuck_at_bureau13.cc.uky.edu)
Date: Mon Jan 26 2004 - 12:16:30 CST
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I am installing AMBER on an HP ia64 system. I also installed the MOPAC
version from http://comp.chem.umn.edu/mopac/. When doing the antechamber tests,
several diffs show relatively large differences ( e.g. 6.04980360E+00 vs.
6.10447050E+00 in the prmtop files). I am including the problematic diff
files from the ash test in this email. Are these tests within acceptable
limits, or does this indicate a problem? If the latter, can you give me any pointer as to what needs to be done?
Thanks
Chuck Fisher
Sr. Systems Programmer
University of Kentucky
---------------------------------mdout.dif------------------------------------
49c49
< Sum of charges from parm topology file = -0.00200000
--- > Sum of charges from parm topology file = 0.00200000 58c58 < 1 -2.9300E+01 3.9152E+01 1.6662E+02 N 13 --- > 1 -2.9999E+01 3.9150E+01 1.6667E+02 N 13 60,61c60,61 < VDWAALS = 44.3868 EEL = -113.3509 HBOND = 0.0000 < 1-4 VDW = 6.1536 1-4 EEL = 13.7526 RESTRAINT = 0.0000 --- > VDWAALS = 44.3868 EEL = -113.7525 HBOND = 0.0000 > 1-4 VDW = 6.1536 1-4 EEL = 13.4556 RESTRAINT = 0.0000 63,66c63,66 < 2 -3.3172E+01 3.5425E+01 1.5261E+02 N 13 < BOND = 1.9888 ANGLE = 3.5338 DIHED = 13.6680 < VDWAALS = 41.1787 EEL = -113.3172 HBOND = 0.0000 < 1-4 VDW = 6.0862 1-4 EEL = 13.6896 RESTRAINT = 0.0000 --- > 2 -3.3870E+01 3.5424E+01 1.5264E+02 N 13 > BOND = 1.9890 ANGLE = 3.5338 DIHED = 13.6679 > VDWAALS = 41.1788 EEL = -113.7188 HBOND = 0.0000 > 1-4 VDW = 6.0863 1-4 EEL = 13.3925 RESTRAINT = 0.0000 68,71c68,71 < 3 -3.7331E+01 3.1369E+01 1.3723E+02 N 13 < BOND = 1.7017 ANGLE = 3.2895 DIHED = 13.6772 < VDWAALS = 37.6605 EEL = -113.2722 HBOND = 0.0000 < 1-4 VDW = 6.0048 1-4 EEL = 13.6074 RESTRAINT = 0.0000 --- > 3 -3.8029E+01 3.1368E+01 1.3727E+02 N 13 > BOND = 1.7021 ANGLE = 3.2895 DIHED = 13.6772 > VDWAALS = 37.6606 EEL = -113.6738 HBOND = 0.0000 > 1-4 VDW = 6.0048 1-4 EEL = 13.3101 RESTRAINT = 0.0000 73,76c73,76 < 4 -4.1695E+01 2.7090E+01 1.2064E+02 N 13 < BOND = 1.4933 ANGLE = 3.0499 DIHED = 13.6985 < VDWAALS = 33.8699 EEL = -113.2108 HBOND = 0.0000 < 1-4 VDW = 5.9062 1-4 EEL = 13.4979 RESTRAINT = 0.0000 --- > 4 -4.2393E+01 2.7089E+01 1.2068E+02 N 13 > BOND = 1.4940 ANGLE = 3.0499 DIHED = 13.6985 > VDWAALS = 33.8702 EEL = -113.6126 HBOND = 0.0000 > 1-4 VDW = 5.9063 1-4 EEL = 13.2004 RESTRAINT = 0.0000 78,81c78,81 < 5 -4.6155E+01 2.2783E+01 1.0312E+02 N 13 < BOND = 1.3884 ANGLE = 2.8311 DIHED = 13.7385 < VDWAALS = 29.8764 EEL = -113.1254 HBOND = 0.0000 < 1-4 VDW = 5.7868 1-4 EEL = 13.3488 RESTRAINT = 0.0000 --- > 5 -4.6853E+01 2.2783E+01 1.0316E+02 N 13 > BOND = 1.3893 ANGLE = 2.8312 DIHED = 13.7385 > VDWAALS = 29.8769 EEL = -113.5273 HBOND = 0.0000 > 1-4 VDW = 5.7870 1-4 EEL = 13.0511 RESTRAINT = 0.0000 83,86c83,86 < 6 -5.0600E+01 1.8742E+01 8.5150E+01 N 13 < BOND = 1.3737 ANGLE = 2.6486 DIHED = 13.8058 < VDWAALS = 25.7911 EEL = -113.0038 HBOND = 0.0000 < 1-4 VDW = 5.6431 1-4 EEL = 13.1415 RESTRAINT = 0.0000 --- > 6 -5.1298E+01 1.8743E+01 8.5187E+01 N 13 > BOND = 1.3748 ANGLE = 2.6488 DIHED = 13.8058 > VDWAALS = 25.7919 EEL = -113.4059 HBOND = 0.0000 > 1-4 VDW = 5.6433 1-4 EEL = 12.8432 RESTRAINT = 0.0000 88,91c88,91 < 7 -5.4957E+01 1.5255E+01 6.7458E+01 N 13 < BOND = 1.3612 ANGLE = 2.5077 DIHED = 13.9095 < VDWAALS = 21.7732 EEL = -112.8288 HBOND = 0.0000 < 1-4 VDW = 5.4721 1-4 EEL = 12.8487 RESTRAINT = 0.0000 --- > 7 -5.5655E+01 1.5256E+01 6.7494E+01 N 13 > BOND = 1.3624 ANGLE = 2.5082 DIHED = 13.9095 > VDWAALS = 21.7743 EEL = -113.2312 HBOND = 0.0000 > 1-4 VDW = 5.4724 1-4 EEL = 12.5496 RESTRAINT = 0.0000 93,96c93,96 < 8 -5.9203E+01 1.2355E+01 5.0979E+01 N 13 < BOND = 1.2169 ANGLE = 2.3988 DIHED = 14.0547 < VDWAALS = 17.9964 EEL = -112.5797 HBOND = 0.0000 < 1-4 VDW = 5.2733 1-4 EEL = 12.4361 RESTRAINT = 0.0000 --- > 8 -5.9902E+01 1.2356E+01 5.1014E+01 N 13 > BOND = 1.2183 ANGLE = 2.3997 DIHED = 14.0549 > VDWAALS = 17.9979 EEL = -112.9826 HBOND = 0.0000 > 1-4 VDW = 5.2738 1-4 EEL = 12.1360 RESTRAINT = 0.0000 98,101c98,101 < 9 -6.3301E+01 9.8241E+00 3.6385E+01 N 13 < BOND = 0.9345 ANGLE = 2.3175 DIHED = 14.2384 < VDWAALS = 14.5358 EEL = -112.2376 HBOND = 0.0000 < 1-4 VDW = 5.0448 1-4 EEL = 11.8655 RESTRAINT = 0.0000 --- > 9 -6.4000E+01 9.8247E+00 3.6417E+01 N 13 > BOND = 0.9363 ANGLE = 2.3191 DIHED = 14.2387 > VDWAALS = 14.5376 EEL = -112.6411 HBOND = 0.0000 > 1-4 VDW = 5.0454 1-4 EEL = 11.5641 RESTRAINT = 0.0000 103,106c103,106 < 10 -6.7158E+01 7.6144E+00 2.3760E+01 N 13 < BOND = 0.6998 ANGLE = 2.2856 DIHED = 14.4525 < VDWAALS = 11.3200 EEL = -111.7860 HBOND = 0.0000 < 1-4 VDW = 4.7759 1-4 EEL = 11.0943 RESTRAINT = 0.0000 --- > 10 -6.7857E+01 7.6147E+00 2.3788E+01 N 13 > BOND = 0.7022 ANGLE = 2.2879 DIHED = 14.4530 > VDWAALS = 11.3221 EEL = -112.1903 HBOND = 0.0000 > 1-4 VDW = 4.7768 1-4 EEL = 10.7914 RESTRAINT = 0.0000 108,111c108,111 < 11 -7.0704E+01 5.7768E+00 1.7127E+01 CG 22 < BOND = 0.6073 ANGLE = 2.3018 DIHED = 14.6817 < VDWAALS = 8.3657 EEL = -111.2129 HBOND = 0.0000 < 1-4 VDW = 4.4606 1-4 EEL = 10.0922 RESTRAINT = 0.0000 --- > 11 -7.1403E+01 5.7773E+00 1.7153E+01 CG 22 > BOND = 0.6099 ANGLE = 2.3050 DIHED = 14.6826 > VDWAALS = 8.3681 EEL = -111.6183 HBOND = 0.0000 > 1-4 VDW = 4.4618 1-4 EEL = 9.7880 RESTRAINT = 0.0000 113,116c113,116 < 12 -7.1664E+01 5.3321E+00 1.5441E+01 CG 22 < BOND = 0.5875 ANGLE = 2.2871 DIHED = 14.7322 < VDWAALS = 7.6354 EEL = -111.0329 HBOND = 0.0000 < 1-4 VDW = 4.3665 1-4 EEL = 9.7601 RESTRAINT = 0.0000 --- > 12 -7.2363E+01 5.3328E+00 1.5465E+01 CG 22 > BOND = 0.5901 ANGLE = 2.2904 DIHED = 14.7333 > VDWAALS = 7.6379 EEL = -111.4387 HBOND = 0.0000 > 1-4 VDW = 4.3678 1-4 EEL = 9.4557 RESTRAINT = 0.0000 118,121c118,121 < 13 -7.7244E+01 3.6636E+00 1.2555E+01 HD2 24 < BOND = 0.7940 ANGLE = 2.8100 DIHED = 15.4458 < VDWAALS = 2.7537 EEL = -109.3828 HBOND = 0.0000 < 1-4 VDW = 3.6193 1-4 EEL = 6.7164 RESTRAINT = 0.0000 --- > 13 -7.7944E+01 3.6658E+00 1.2563E+01 HD2 24 > BOND = 0.7957 ANGLE = 2.8147 DIHED = 15.4489 > VDWAALS = 2.7568 EEL = -109.7919 HBOND = 0.0000 > 1-4 VDW = 3.6216 1-4 EEL = 6.4104 RESTRAINT = 0.0000 123,126c123,126 < 14 -7.8131E+01 5.4521E+00 1.7358E+01 CG 22 < BOND = 1.3695 ANGLE = 3.6330 DIHED = 16.0468 < VDWAALS = 1.0155 EEL = -108.4377 HBOND = 0.0000 < 1-4 VDW = 3.2699 1-4 EEL = 4.9724 RESTRAINT = 0.0000 --- > 14 -7.8831E+01 5.4573E+00 1.7423E+01 CG 22 > BOND = 1.3704 ANGLE = 3.6391 DIHED = 16.0514 > VDWAALS = 1.0184 EEL = -108.8482 HBOND = 0.0000 > 1-4 VDW = 3.2726 1-4 EEL = 4.6655 RESTRAINT = 0.0000 128,131c128,131 < 15 -3.2346E+01 5.8460E+01 2.3532E+02 CG 22 < BOND = 40.2142 ANGLE = 18.7427 DIHED = 16.4821 < VDWAALS = -1.8833 EEL = -107.1785 HBOND = 0.0000 < 1-4 VDW = 2.4053 1-4 EEL = -1.1281 RESTRAINT = 0.0000 --- > 15 -3.3013E+01 5.8487E+01 2.3574E+02 CG 22 > BOND = 40.2535 ANGLE = 18.7535 DIHED = 16.4940 > VDWAALS = -1.8838 EEL = -107.5924 HBOND = 0.0000 > 1-4 VDW = 2.4090 1-4 EEL = -1.4467 RESTRAINT = 0.0000 133,136c133,136 < 16 -7.8895E+01 4.4690E+00 1.5751E+01 CG 22 < BOND = 1.2133 ANGLE = 4.1501 DIHED = 16.0295 < VDWAALS = 0.5156 EEL = -108.2836 HBOND = 0.0000 < 1-4 VDW = 3.1576 1-4 EEL = 4.3229 RESTRAINT = 0.0000 --- > 16 -7.9596E+01 4.4746E+00 1.5774E+01 CG 22 > BOND = 1.2149 ANGLE = 4.1557 DIHED = 16.0349 > VDWAALS = 0.5176 EEL = -108.6941 HBOND = 0.0000 > 1-4 VDW = 3.1603 1-4 EEL = 4.0145 RESTRAINT = 0.0000 138,141c138,141 < 17 -7.9751E+01 3.6316E+00 1.0523E+01 CG 22 < BOND = 1.1522 ANGLE = 4.1053 DIHED = 15.7922 < VDWAALS = 0.3645 EEL = -108.3155 HBOND = 0.0000 < 1-4 VDW = 3.1563 1-4 EEL = 3.9944 RESTRAINT = 0.0000 --- > 17 -8.0454E+01 3.6361E+00 1.0545E+01 CG 22 > BOND = 1.1547 ANGLE = 4.1096 DIHED = 15.7979 > VDWAALS = 0.3659 EEL = -108.7265 HBOND = 0.0000 > 1-4 VDW = 3.1592 1-4 EEL = 3.6848 RESTRAINT = 0.0000 143,146c143,146 < 18 -8.0654E+01 5.2355E+00 1.5368E+01 N 13 < BOND = 1.5355 ANGLE = 4.4962 DIHED = 15.3757 < VDWAALS = 0.0156 EEL = -108.3980 HBOND = 0.0000 < 1-4 VDW = 3.1612 1-4 EEL = 3.1595 RESTRAINT = 0.0000 --- > 18 -8.1361E+01 5.2388E+00 1.5389E+01 N 13 > BOND = 1.5421 ANGLE = 4.4991 DIHED = 15.3812 > VDWAALS = 0.0153 EEL = -108.8101 HBOND = 0.0000 > 1-4 VDW = 3.1645 1-4 EEL = 2.8466 RESTRAINT = 0.0000 148,151c148,151 < 19 -8.0247E+01 9.7367E+00 3.4444E+01 C 11 < BOND = 2.6610 ANGLE = 5.4199 DIHED = 14.8927 < VDWAALS = 0.2349 EEL = -109.0489 HBOND = 0.0000 < 1-4 VDW = 3.2408 1-4 EEL = 2.3528 RESTRAINT = 0.0000 --- > 19 -8.0952E+01 9.7560E+00 3.4554E+01 C 11 > BOND = 2.6699 ANGLE = 5.4271 DIHED = 14.8970 > VDWAALS = 0.2346 EEL = -109.4637 HBOND = 0.0000 > 1-4 VDW = 3.2449 1-4 EEL = 2.0383 RESTRAINT = 0.0000 153,156c153,156 < 20 -8.1444E+01 3.3357E+00 8.5040E+00 OD2 23 < BOND = 1.3597 ANGLE = 4.7113 DIHED = 15.0908 < VDWAALS = 0.1024 EEL = -108.6899 HBOND = 0.0000 < 1-4 VDW = 3.1887 1-4 EEL = 2.7932 RESTRAINT = 0.0000 --- > 20 -8.2153E+01 3.3444E+00 8.5295E+00 OD2 23 > BOND = 1.3652 ANGLE = 4.7151 DIHED = 15.0959 > VDWAALS = 0.1020 EEL = -109.1031 HBOND = 0.0000 > 1-4 VDW = 3.1923 1-4 EEL = 2.4796 RESTRAINT = 0.0000 160,163c160,163 < 20 -8.1444E+01 3.3357E+00 8.5040E+00 OD2 23 < BOND = 1.3597 ANGLE = 4.7113 DIHED = 15.0908 < VDWAALS = 0.1024 EEL = -108.6899 HBOND = 0.0000 < 1-4 VDW = 3.1887 1-4 EEL = 2.7932 RESTRAINT = 0.0000 --- > 20 -8.2153E+01 3.3444E+00 8.5295E+00 OD2 23 > BOND = 1.3652 ANGLE = 4.7151 DIHED = 15.0959 > VDWAALS = 0.1020 EEL = -109.1031 HBOND = 0.0000 > 1-4 VDW = 3.1923 1-4 EEL = 2.4796 RESTRAINT = 0.0000---------------------------prmtop.dif----------------------------------------
16,20c16,20 < -3.13423560E+00 1.45778400E+00 1.25733870E+00 1.11156030E+00 1.19902734E+01 < -1.10973807E+01 -1.03684887E+01 6.04980360E+00 8.92892700E-01 1.84045230E+00 < 1.16987166E+01 -1.12978260E+01 -1.01133765E+01 6.12269280E+00 1.34845020E+00 < 1.36667250E+00 6.56002800E-01 5.83113600E-01 -2.89734570E+00 2.09556450E+00 < 1.78578540E+00 1.17716058E+01 -1.09151577E+01 8.18181270E+00 -1.04231556E+01 --- > -3.13423560E+00 1.45778400E+00 1.23911640E+00 1.11156030E+00 1.20267180E+01 > -1.11156030E+01 -1.04231556E+01 6.10447050E+00 9.65781900E-01 1.85867460E+00 > 1.16987166E+01 -1.13342706E+01 -1.01315988E+01 6.15913740E+00 1.36667250E+00 > 1.38489480E+00 6.56002800E-01 5.64891300E-01 -2.93379030E+00 2.09556450E+00 > 1.78578540E+00 1.18080504E+01 -1.09333800E+01 8.18181270E+00 -1.04231556E+01
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- Reply: David A. Case: "Re: AMBER: installation test question (antechamber, ash)"
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