AMBER Archive (2006)

Subject: AMBER: antechamber charge calculation very sensitive to conformations ?

From: Christophe Guilbert (cguilbert_at_picasso.ucsf.edu)
Date: Wed Aug 23 2006 - 20:59:08 CDT

Dear Amber(l)ist ,

I found that charges calculated with Antechamber/mopac (v1.25) on two
very close ligand conformation (RMSD = 0.45A) could lead to some
surprising different charges on Atoms.

antechamber -nc 5 -rn lig -i liga_regul.pdb -fi pdb -o liga_regul.mol2
-fo mol2 -c bcc -j 4 -at gaff -pf y
antechamber -nc 5 -rn lig -i lig_mini.pdb -fi pdb -o lig_mini.mol2 -fo
mol2 -c bcc -j 4 -at gaff -pf y

Please find in the attachment the mol2 files "liga_regul.mol2" and
"lig_mini.mol2" , H7 (from NH3+) has a charge of +0.05 in
"liga_regul.mol2" where is it +0.48 in "lig_mini.mol2".

Graphicaly looking to these conformations, I can't understand why H7
charge is so different , and moreover its charge is different than the
two other H in -NH3+ (HN51, HN52)
It looks like it is structure dependent, if you start again from the
previous mol2 files , you have the same result and charge different for H7.
antechamber -nc 5 -rn lig -i liga_regul.mol2 -fi mol2 -o
liga_regul_NEW.mol2 -fo mol2 -c bcc -j 4 -at gaff -pf y
antechamber -nc 5 -rn lig -i lig_mini.mol2 -fi mol2 -o
lig_mini_NEW.mol2 -fo mol2 -c bcc -j 4 -at gaff -pf y

My question is the following:
1) It is normal to find such charges difference for a slightly
ddifferent conformation ?? If so , I guess, it would be a good idea to
first optimize (I thought MOPAC would do it) the conformation before
calculating the charges with Antechamber.

Thanks a lot for any thought.

Chris 

-- 
--------------------------------------------------------------------------
Christophe Guilbert, Ph.D.
Mission Bay Genentech Hall
UCSF, Department of Pharmaceutical Chemistry
600 16th Street, Suite # S-126-D
Genentech Hall, Mail Code 2280 
San Francisco, CA  94158-2517 
for UPS/Fed Ex/DHL, change the zip code of 94107 for physical deliveries of package
Office      : 415-476-0707
Office fax  : 415-476-0688
Email: cguilbert_at_picasso.ucsf.edu
http://mondale.ucsf.edu
--------------------------------------------------------------------------
In a world without walls and fences,
who needs Windows and Gates?
        - Sun Microsystems

@<TRIPOS>MOLECULE
lig
   92 95 1 0 0
SMALL
bcc

@<TRIPOS>ATOM
      1 C1 1.9800 -0.8790 43.9990 c3 1 lig 0.4593
      2 O1 1.7640 -2.2970 44.2130 os 1 lig -0.5178
      3 C2 3.3160 -0.4070 44.6850 c3 1 lig -0.6210
      4 N2 4.4410 -1.3420 44.5370 n4 1 lig -1.1753
      5 H6 4.6350 -1.4880 43.5580 hn 1 lig 0.3529
      6 HN21 5.2560 -0.9820 45.0110 hn 1 lig 0.3165
      7 HN22 4.2260 -2.2170 44.9920 hn 1 lig 0.3395
      8 H2 3.6040 0.5590 44.2330 hx 1 lig 0.0507
      9 C3 3.1310 -0.1920 46.1990 c3 1 lig 0.2895
     10 O3 4.2580 0.4810 46.7560 oh 1 lig -0.6568
     11 HO3 4.2980 1.3360 46.3200 ho 1 lig 0.3737
     12 H3 3.0440 -1.1880 46.6490 h1 1 lig -0.0074
     13 C4 1.8580 0.6170 46.4900 c3 1 lig 0.1075
     14 O4 1.7270 0.8430 47.8900 oh 1 lig -0.6774
     15 HO4 1.6440 -0.0260 48.2910 ho 1 lig 0.4363
     16 H4 1.9660 1.5640 45.9450 h1 1 lig 0.0139
     17 C5 0.6180 -0.0770 45.8840 c3 1 lig 0.0695
     18 C6 -0.6990 0.6520 46.1450 c3 1 lig 0.2965
     19 O6 -1.0350 0.6300 47.5260 oh 1 lig -1.0617
     20 HO6 -1.1060 -0.2970 47.7670 ho 1 lig 0.3305
     21 H61 -1.5030 0.1790 45.5550 h1 1 lig -0.1059
     22 H62 -0.6390 1.6910 45.7970 h1 1 lig -0.1179
     23 H5 0.5190 -1.1120 46.2440 h1 1 lig 0.0105
     24 O5 0.8220 -0.1270 44.4560 os 1 lig -0.4666
     25 H1 2.0090 -0.6590 42.9210 h2 1 lig 0.0388
     26 C7 0.2340 -5.6030 41.9910 c3 1 lig 0.1414
     27 N1 -0.5220 -6.5150 41.1210 n4 1 lig -1.1116
     28 H8 -0.9790 -7.2190 41.6790 hn 1 lig -0.7952
     29 HN11 -1.1980 -5.9960 40.5790 hn 1 lig 0.3486
     30 HN12 0.0970 -6.9430 40.4460 hn 1 lig 0.3557
     31 C10 1.0020 -4.5150 41.1810 c3 1 lig 0.1249
     32 O2 1.9150 -5.1240 40.2710 oh 1 lig -0.5978
     33 HO2 2.5300 -5.6270 40.8100 ho 1 lig 0.3864
     34 H11 0.2770 -3.9180 40.5900 h1 1 lig 0.0985
     35 C13 1.8040 -3.5700 42.1230 c3 1 lig 0.1007
     36 O8 2.3580 -2.4800 41.3280 os 1 lig -0.4166
     37 H14 2.6090 -4.1660 42.5970 h1 1 lig 0.0407
     38 C16 0.9110 -2.9800 43.2630 c3 1 lig 0.1179
     39 H17 0.1840 -2.2740 42.8090 h1 1 lig 0.0581
     40 C19 0.1050 -4.0760 44.0310 c3 1 lig 0.1508
     41 N5 -0.7980 -3.4840 45.0280 n4 1 lig -1.0991
     42 H7 -1.2870 -4.2140 45.5220 hn 1 lig 0.0529
     43 HN51 -0.2740 -2.9080 45.6720 hn 1 lig 0.3792
     44 HN52 -1.4510 -2.8600 44.5770 hn 1 lig 0.3348
     45 H24 0.8170 -4.7280 44.5730 hx 1 lig 0.0384
     46 C22 -0.7100 -4.9490 43.0420 c3 1 lig -0.0708
     47 H20 -1.3020 -5.7250 43.5610 hc 1 lig 0.0387
     48 H22 -1.4760 -4.3040 42.5710 hc 1 lig 0.0445
     49 H26 0.9750 -6.2230 42.5320 hx 1 lig 0.0027
     50 C8 3.8050 -2.2640 41.2910 c3 1 lig 0.2878
     51 C11 4.2580 -2.2090 39.8200 c3 1 lig 0.0584
     52 O13 5.6280 -2.5790 39.6920 oh 1 lig -0.5711
     53 H29 5.6790 -3.5010 39.9530 ho 1 lig 0.3826
     54 H12 3.6380 -2.8450 39.1610 h1 1 lig 0.0517
     55 C14 4.0320 -0.7130 39.5540 c3 1 lig 0.1513
     56 H15 2.9320 -0.5430 39.5340 h1 1 lig 0.0798
     57 C17 4.5760 -0.0720 40.8200 c3 1 lig 0.0749
     58 C20 4.0650 1.3460 41.1060 c3 1 lig 0.1340
     59 O11 4.6930 1.8650 42.2690 oh 1 lig -0.6385
     60 HO5 5.6270 1.6710 42.1730 ho 1 lig 0.4024
     61 H51 2.9660 1.3560 41.2380 h1 1 lig 0.0425
     62 H52 4.2900 2.0060 40.2510 h1 1 lig 0.1105
     63 H18 5.6840 -0.0650 40.8010 h1 1 lig 0.0574
     64 O9 4.1310 -0.9690 41.8260 os 1 lig -0.4185
     65 H27 4.3300 -3.0100 41.9160 h2 1 lig 0.0850
     66 C9 2.4950 2.6990 36.0170 c3 1 lig 0.0924
     67 O7 3.2120 3.8370 36.4920 oh 1 lig -0.6607
     68 HO1 3.8940 3.4960 37.0750 ho 1 lig 0.4202
     69 C12 3.4670 1.7620 35.2470 c3 1 lig 0.2890
     70 O14 2.6960 0.8460 34.4730 oh 1 lig -0.7286
     71 H30 2.1340 1.3830 33.9110 ho 1 lig 0.3809
     72 H13 4.0350 2.3850 34.5380 h1 1 lig -0.0229
     73 C15 4.4640 0.9520 36.1390 c3 1 lig -0.6325
     74 N3 5.6540 1.7610 36.4390 n4 1 lig -1.1932
     75 H10 5.3880 2.5760 36.9690 hn 1 lig 0.3671
     76 HN31 6.3290 1.2080 36.9490 hn 1 lig 0.3348
     77 HN32 6.1160 2.0290 35.5820 hn 1 lig 0.3216
     78 H16 4.7830 0.0660 35.5660 hx 1 lig 0.0547
     79 C18 3.7780 0.3970 37.4150 c3 1 lig 0.4752
     80 O10 4.6970 -0.1750 38.3780 os 1 lig -0.4101
     81 H19 3.1620 -0.4470 37.0960 h2 1 lig -0.0718
     82 O12 2.9390 1.4290 38.0350 os 1 lig -0.5073
     83 C21 1.8580 1.9320 37.2030 c3 1 lig 0.3138
     84 C23 0.8710 2.7750 38.0320 c3 1 lig -0.6700
     85 N6 0.2440 2.0090 39.1190 n4 1 lig -1.1865
     86 H9 0.9530 1.6620 39.7450 hn 1 lig 0.3649
     87 HN61 -0.2980 1.2470 38.7370 hn 1 lig 0.3389
     88 HN62 -0.4170 2.5900 39.6150 hn 1 lig 0.3099
     89 H21 1.3950 3.6450 38.4550 hx 1 lig 0.0163
     90 H23 0.0770 3.1830 37.3800 hx 1 lig -0.0041
     91 H25 1.2890 1.0780 36.7890 h1 1 lig -0.0768
     92 H28 1.7040 3.0540 35.3310 h1 1 lig -0.0070
@<TRIPOS>BOND
     1 1 2 1
     2 1 3 1
     3 1 24 1
     4 1 25 1
     5 2 38 1
     6 3 4 1
     7 3 8 1
     8 3 9 1
     9 4 5 1
    10 4 6 1
    11 4 7 1
    12 9 10 1
    13 9 12 1
    14 9 13 1
    15 10 11 1
    16 13 14 1
    17 13 16 1
    18 13 17 1
    19 14 15 1
    20 17 18 1
    21 17 23 1
    22 17 24 1
    23 18 19 1
    24 18 21 1
    25 18 22 1
    26 19 20 1
    27 26 27 1
    28 26 31 1
    29 26 46 1
    30 26 49 1
    31 27 28 1
    32 27 29 1
    33 27 30 1
    34 31 32 1
    35 31 34 1
    36 31 35 1
    37 32 33 1
    38 35 36 1
    39 35 37 1
    40 35 38 1
    41 36 50 1
    42 38 39 1
    43 38 40 1
    44 40 41 1
    45 40 45 1
    46 40 46 1
    47 41 42 1
    48 41 43 1
    49 41 44 1
    50 46 47 1
    51 46 48 1
    52 50 51 1
    53 50 64 1
    54 50 65 1
    55 51 52 1
    56 51 54 1
    57 51 55 1
    58 52 53 1
    59 55 56 1
    60 55 57 1
    61 55 80 1
    62 57 58 1
    63 57 63 1
    64 57 64 1
    65 58 59 1
    66 58 61 1
    67 58 62 1
    68 59 60 1
    69 66 67 1
    70 66 69 1
    71 66 83 1
    72 66 92 1
    73 67 68 1
    74 69 70 1
    75 69 72 1
    76 69 73 1
    77 70 71 1
    78 73 74 1
    79 73 78 1
    80 73 79 1
    81 74 75 1
    82 74 76 1
    83 74 77 1
    84 79 80 1
    85 79 81 1
    86 79 82 1
    87 82 83 1
    88 83 84 1
    89 83 91 1
    90 84 85 1
    91 84 89 1
    92 84 90 1
    93 85 86 1
    94 85 87 1
    95 85 88 1
@<TRIPOS>SUBSTRUCTURE
     1 lig 1 TEMP 0 **** **** 0 ROOT


@<TRIPOS>MOLECULE
lig
   92 95 1 0 0
SMALL
bcc

@<TRIPOS>ATOM
      1 C1 1.7350 -0.7640 43.9060 c3 1 lig 0.3286
      2 O1 1.6110 -2.1650 44.2510 os 1 lig -0.4773
      3 C2 2.9530 -0.1870 44.6750 c3 1 lig 0.0933
      4 N2 4.2330 -0.9650 44.4700 n4 1 lig -0.8244
      5 H6 4.9920 -0.5160 45.0140 hn 1 lig 0.4966
      6 HN21 4.5360 -0.9580 43.4820 hn 1 lig 0.4857
      7 HN22 4.1820 -1.9650 44.7840 hn 1 lig 0.4541
      8 H2 3.1240 0.8400 44.3360 hx 1 lig 0.1555
      9 C3 2.7040 -0.1830 46.1860 c3 1 lig 0.1231
     10 O3 3.9070 0.3110 46.7860 oh 1 lig -0.6128
     11 HO3 3.8410 0.3270 47.7840 ho 1 lig 0.4870
     12 H3 2.4970 -1.1980 46.5340 h1 1 lig 0.0824
     13 C4 1.4770 0.7000 46.4530 c3 1 lig 0.1029
     14 O4 1.2350 0.8060 47.8530 oh 1 lig -0.5727
     15 HO4 0.2580 0.9580 47.9390 ho 1 lig 0.4609
     16 H4 1.6500 1.6920 46.0440 h1 1 lig 0.0996
     17 C5 0.2550 0.0730 45.7330 c3 1 lig 0.0957
     18 C6 -1.0230 0.9220 45.9260 c3 1 lig 0.1364
     19 O6 -1.4480 0.8990 47.3010 oh 1 lig -0.6969
     20 HO6 -2.4390 0.7570 47.3090 ho 1 lig 0.4734
     21 H61 -1.8190 0.5310 45.2860 h1 1 lig 0.0881
     22 H62 -0.8170 1.9500 45.6260 h1 1 lig 0.1019
     23 H5 0.0800 -0.9300 46.1180 h1 1 lig 0.0594
     24 O5 0.5350 -0.0330 44.3030 os 1 lig -0.4431
     25 H1 1.8790 -0.6620 42.8210 h2 1 lig 0.1135
     26 C7 0.9410 -5.8400 42.2090 c3 1 lig 0.1273
     27 N1 0.3620 -6.8900 41.3030 n4 1 lig -0.8351
     28 H8 -0.2690 -6.5290 40.5630 hn 1 lig 0.4725
     29 HN11 -0.1340 -7.6530 41.7950 hn 1 lig 0.4896
     30 HN12 1.1100 -7.3940 40.7570 hn 1 lig 0.5004
     31 C10 1.5910 -4.7180 41.3680 c3 1 lig 0.1006
     32 O2 2.6990 -5.3260 40.6870 oh 1 lig -0.6095
     33 HO2 3.0530 -4.7180 39.9890 ho 1 lig 0.4643
     34 H11 0.8520 -4.3360 40.6560 h1 1 lig 0.0926
     35 C13 2.0870 -3.5290 42.2400 c3 1 lig 0.1111
     36 O8 2.4380 -2.4570 41.3230 os 1 lig -0.4308
     37 H14 2.9650 -3.8440 42.8070 h1 1 lig 0.0981
     38 C16 1.0110 -3.0410 43.2600 c3 1 lig 0.1395
     39 H17 0.1870 -2.5350 42.7470 h1 1 lig 0.1073
     40 C19 0.4960 -4.2640 44.0530 c3 1 lig 0.1196
     41 N5 -0.4750 -3.9070 45.1410 n4 1 lig -0.8326
     42 H7 -0.7560 -4.7680 45.6430 hn 1 lig 0.4809
     43 HN51 -1.3320 -3.4380 44.7840 hn 1 lig 0.4829
     44 HN52 -0.0250 -3.2870 45.8660 hn 1 lig 0.4991
     45 H24 1.3490 -4.7380 44.5470 hx 1 lig 0.1357
     46 C22 -0.1650 -5.2660 43.1030 c3 1 lig -0.1389
     47 H20 -0.6450 -6.0590 43.6730 hc 1 lig 0.1130
     48 H22 -0.9380 -4.7840 42.5010 hc 1 lig 0.1040
     49 H26 1.7130 -6.3270 42.8190 hx 1 lig 0.1389
     50 C8 3.8500 -2.2220 41.1160 c3 1 lig 0.2901
     51 C11 4.1220 -1.9870 39.6200 c3 1 lig 0.0791
     52 O13 5.4310 -2.4700 39.2960 oh 1 lig -0.5745
     53 H29 5.6870 -2.0810 38.4180 ho 1 lig 0.4249
     54 H12 3.3610 -2.4590 38.9940 h1 1 lig 0.1298
     55 C14 4.0600 -0.4630 39.5380 c3 1 lig 0.1029
     56 H15 3.0140 -0.1640 39.6090 h1 1 lig 0.1063
     57 C17 4.7690 -0.0310 40.8160 c3 1 lig 0.1033
     58 C20 4.4830 1.4460 41.1620 c3 1 lig 0.1248
     59 O11 4.3890 1.6670 42.5720 oh 1 lig -0.6471
     60 HO5 5.2420 1.4600 43.0480 ho 1 lig 0.4555
     61 H51 3.5450 1.7570 40.7000 h1 1 lig 0.0767
     62 H52 5.2750 2.0670 40.7420 h1 1 lig 0.0780
     63 H18 5.8460 -0.2050 40.7330 h1 1 lig 0.1074
     64 O9 4.1970 -0.9690 41.7630 os 1 lig -0.4522
     65 H27 4.4460 -3.0550 41.5220 h2 1 lig 0.1054
     66 C9 2.5340 2.7710 35.8570 c3 1 lig 0.0595
     67 O7 3.2840 3.9340 36.2510 oh 1 lig -0.6429
     68 HO1 3.3860 4.5280 35.4540 ho 1 lig 0.4653
     69 C12 3.4540 1.7290 35.1610 c3 1 lig 0.1168
     70 O14 2.6420 0.6700 34.6350 oh 1 lig -0.5877
     71 H30 2.9940 0.4230 33.7360 ho 1 lig 0.4762
     72 H13 3.9970 2.2110 34.3380 h1 1 lig 0.1033
     73 C15 4.4680 1.1170 36.1590 c3 1 lig 0.0716
     74 N3 5.4590 2.1810 36.5880 n4 1 lig -0.8301
     75 H10 4.9690 3.0880 36.7030 hn 1 lig 0.4841
     76 HN31 6.2360 2.2980 35.9050 hn 1 lig 0.4813
     77 HN32 5.9050 1.9710 37.5180 hn 1 lig 0.4769
     78 H16 5.0240 0.2970 35.6890 hx 1 lig 0.1455
     79 C18 3.7000 0.5800 37.3870 c3 1 lig 0.3319
     80 O10 4.6600 0.0730 38.3380 os 1 lig -0.4371
     81 H19 3.0280 -0.2410 37.0930 h2 1 lig 0.1386
     82 O12 2.9020 1.6390 37.9910 os 1 lig -0.4453
     83 C21 1.8660 2.1910 37.1270 c3 1 lig 0.1356
     84 C23 1.1280 3.3130 37.8810 c3 1 lig 0.1052
     85 N6 0.5060 2.7910 39.1430 n4 1 lig -0.8344
     86 H9 1.0280 2.0170 39.6220 hn 1 lig 0.4734
     87 HN61 -0.4430 2.4420 38.9550 hn 1 lig 0.4752
     88 HN62 0.3920 3.5810 39.8160 hn 1 lig 0.4979
     89 H21 0.3300 3.7530 37.2770 hx 1 lig 0.1364
     90 H23 1.8350 4.1070 38.1410 hx 1 lig 0.1348
     91 H25 1.1580 1.4040 36.8480 h1 1 lig 0.1125
     92 H28 1.7540 3.0680 35.1470 h1 1 lig 0.1035
@<TRIPOS>BOND
     1 1 2 1
     2 1 3 1
     3 1 24 1
     4 1 25 1
     5 2 38 1
     6 3 4 1
     7 3 8 1
     8 3 9 1
     9 4 5 1
    10 4 6 1
    11 4 7 1
    12 9 10 1
    13 9 12 1
    14 9 13 1
    15 10 11 1
    16 13 14 1
    17 13 16 1
    18 13 17 1
    19 14 15 1
    20 17 18 1
    21 17 23 1
    22 17 24 1
    23 18 19 1
    24 18 21 1
    25 18 22 1
    26 19 20 1
    27 26 27 1
    28 26 31 1
    29 26 46 1
    30 26 49 1
    31 27 28 1
    32 27 29 1
    33 27 30 1
    34 31 32 1
    35 31 34 1
    36 31 35 1
    37 32 33 1
    38 35 36 1
    39 35 37 1
    40 35 38 1
    41 36 50 1
    42 38 39 1
    43 38 40 1
    44 40 41 1
    45 40 45 1
    46 40 46 1
    47 41 42 1
    48 41 43 1
    49 41 44 1
    50 46 47 1
    51 46 48 1
    52 50 51 1
    53 50 64 1
    54 50 65 1
    55 51 52 1
    56 51 54 1
    57 51 55 1
    58 52 53 1
    59 55 56 1
    60 55 57 1
    61 55 80 1
    62 57 58 1
    63 57 63 1
    64 57 64 1
    65 58 59 1
    66 58 61 1
    67 58 62 1
    68 59 60 1
    69 66 67 1
    70 66 69 1
    71 66 83 1
    72 66 92 1
    73 67 68 1
    74 69 70 1
    75 69 72 1
    76 69 73 1
    77 70 71 1
    78 73 74 1
    79 73 78 1
    80 73 79 1
    81 74 75 1
    82 74 76 1
    83 74 77 1
    84 79 80 1
    85 79 81 1
    86 79 82 1
    87 82 83 1
    88 83 84 1
    89 83 91 1
    90 84 85 1
    91 84 89 1
    92 84 90 1
    93 85 86 1
    94 85 87 1
    95 85 88 1
@<TRIPOS>SUBSTRUCTURE
     1 lig 1 TEMP 0 **** **** 0 ROOT

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu