[gmx-users] Adding Partial Charges for Small Molecules
Nancy
nancy5villa at gmail.com
Mon Jun 14 05:51:53 CEST 2010
Hi Justin,
Thanks for the useful info.
Nancy
On Sun, Jun 13, 2010 at 8:54 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Nancy wrote:
>
>> Hi All,
>>
>> I am trying to add partial charges to nicotinamide adenine dinucleotide
>> (NAD+), for input to molecular simulations. I have been using the UCSF
>> Chimera program to do this. The total charge on this molecule should be -1
>> (assuming the ionization of NAD+ at pH ~7.0, see attached figure). When I
>> add Gasteiger charges, the total charge sums up incorrectly to 0, even
>> though the net charge specified in the drop-down box is -1. However, using
>> the "AM1-BCC" method, the net charge correctly sums up to -1. The charge
>> model used is "Amber ff99SB". I have also noticed that the partial charges
>> on individual atoms assigned when using the
>>
>
> Sounds like a known issue with Chimera...
>
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-August/001732.html
>
>
> "AM1-BCC" method are generally of greater magnitude compared to charges
>> assigned using the Gasteiger method.
>>
>> What is a good way to add correct partial charges to a small molecule?
>>
>>
> The best way is to follow the original methodology of the force field
> itself. The antechamber program of Amber is probably a good place to start
> to get Amber-compatible topologies. Also have a look here:
>
> http://www.pharmacy.manchester.ac.uk/bryce/amber#cof
>
> All of the above will require conversion to Gromacs-compatible formats, but
> there are scripts on the User Contribution site that might be suitable.
>
> -Justin
>
> The mol2 structure code (with incorrect Gasteiger charges) is written
>> below (and attached as NAD.mol2 with corresponding PNG structure image).
>>
>> Thanks in advance,
>> Nancy
>>
>>
>> ============================================================================
>> @<TRIPOS>MOLECULE
>> NAD.mol2
>> 70 74 1 0 0
>> SMALL
>> USER_CHARGES
>>
>>
>> @<TRIPOS>ATOM
>> 1 C1 -1.4117 5.8700 -3.4377 C.2 1 LIG1
>> -0.0471
>> 2 C2 -0.2808 5.1989 -2.9922 C.2 1 LIG1
>> -0.0472
>> 3 C3 0.0698 5.2540 -1.6463 C.2 1 LIG1
>> -0.0021
>> 4 N1 -0.7125 5.8930 -0.7233 N.2 1 LIG1
>> -0.2845
>> 5 C4 -1.7621 6.6431 -1.1880 C.2 1 LIG1
>> 0.0105
>> 6 C5 -2.1590 6.6215 -2.5315 C.2 1 LIG1
>> 0.0510
>> 7 C6 -3.3433 7.3892 -2.9991 C.2 1 LIG1
>> 0.2416
>> 8 O1 -3.7255 7.3875 -4.2002 O.2 1 LIG1
>> -0.2721
>> 9 N2 -4.0978 8.1475 -2.0847 N.3 1 LIG1
>> -0.3250
>> 10 O2 0.0324 4.4339 0.9916 O.3 1 LIG1
>> -0.3484
>> 11 C7 -1.0355 3.6965 1.6402 C.3 1 LIG1
>> 0.1165
>> 12 C8 -1.4243 2.4599 0.8071 C.3 1 LIG1
>> 0.1276
>> 13 O3 -0.4100 1.4351 0.9207 O.3 1 LIG1
>> -0.1602
>> 14 P1 0.8613 1.4216 -0.0633 P.3 1 LIG1
>> 0.5624
>> 15 O4 2.0180 2.1020 0.5580 O.2 1 LIG1
>> -0.3429
>> 16 O5 0.5634 2.0116 -1.3891 O.3 1 LIG1
>> -0.3429
>> 17 O6 1.1223 -0.1529 -0.1877 O.3 1 LIG1
>> 0.0575
>> 18 P2 0.0541 -1.2893 -0.5527 P.3 1 LIG1
>> 0.5624
>> 19 O7 -1.1823 -1.2052 0.2607 O.3 1 LIG1
>> -0.3429
>> 20 O8 0.6340 -2.6390 -0.3765 O.2 1 LIG1
>> -0.3429
>> 21 O9 -0.2208 -1.0077 -2.1109 O.3 1 LIG1
>> -0.1602
>> 22 O10 -2.0844 -2.0838 -4.0533 O.3 1 LIG1
>> -0.3483
>> 23 C9 -1.7580 -0.6726 -3.9721 C.3 1 LIG1
>> 0.1165
>> 24 C10 -1.4291 -0.3206 -2.5098 C.3 1 LIG1
>> 0.1276
>> 25 N3 -5.5165 -1.9977 -1.1853 N.2 1 LIG1
>> -0.2341
>> 26 C11 -5.3009 -1.7637 -2.4944 C.2 1 LIG1
>> 0.0912
>> 27 N4 -4.1259 -2.3733 -2.8716 N.3 1 LIG1
>> -0.2445
>> 28 C12 -3.5825 -3.0679 -1.8327 C.2 1 LIG1
>> 0.1583
>> 29 C13 -4.4622 -2.7976 -0.7674 C.2 1 LIG1
>> 0.1418
>> 30 N5 -2.5159 -3.8010 -1.6563 N.2 1 LIG1
>> -0.2186
>> 31 C14 -2.2518 -4.3018 -0.4707 C.2 1 LIG1
>> 0.1192
>> 32 N6 -3.0604 -4.0697 0.5431 N.2 1 LIG1
>> -0.2228
>> 33 C15 -4.1365 -3.3442 0.4336 C.2 1 LIG1
>> 0.1340
>> 34 N7 -4.8438 -3.2010 1.5627 N.3 1 LIG1
>> -0.2849
>> 35 C16 -2.1891 4.7099 1.7524 C.3 1 LIG1
>> 0.1128
>> 36 C17 -1.4568 6.0605 1.7533 C.3 1 LIG1
>> 0.1256
>> 37 C18 -0.3444 5.8071 0.7094 C.3 1 LIG1
>> 0.1560
>> 38 C19 -3.0362 0.0509 -4.4501 C.3 1 LIG1
>> 0.1128
>> 39 C20 -3.9053 -1.0632 -5.0633 C.3 1 LIG1
>> 0.1257
>> 40 C21 -3.5098 -2.2874 -4.2107 C.3 1 LIG1
>> 0.1588
>> 41 O11 -2.9991 4.5200 2.9209 O.3 1 LIG1
>> -0.3874
>> 42 O12 -0.8413 6.3227 3.0256 O.3 1 LIG1
>> -0.3858
>> 43 O13 -3.5425 -1.3145 -6.4282 O.3 1 LIG1
>> -0.3858
>> 44 O14 -2.7472 1.1126 -5.3700 O.3 1 LIG1
>> -0.3874
>> 45 H1 -1.6809 5.8357 -4.4909 H 1 LIG1
>> 0.0632
>> 46 H2 0.3396 4.6461 -3.6934 H 1 LIG1
>> 0.0636
>> 47 H3 0.9656 4.7572 -1.2733 H 1 LIG1
>> 0.0793
>> 48 H4 -2.2796 7.2615 -0.4632 H 1 LIG1
>> 0.0801
>> 49 H5 -4.8503 8.7190 -2.4374 H 1 LIG1
>> 0.1458
>> 50 H6 -3.7587 8.2854 -1.1465 H 1 LIG1
>> 0.1458
>> 51 H7 -0.6981 3.4004 2.6380 H 1 LIG1
>> 0.0660
>> 52 H8 -1.5845 2.7299 -0.2407 H 1 LIG1
>> 0.0645
>> 53 H9 -2.3510 2.0430 1.2095 H 1 LIG1
>> 0.0645
>> 54 H10 -0.9095 -0.4615 -4.6296 H 1 LIG1
>> 0.0660
>> 55 H11 -1.2870 0.7565 -2.4090 H 1 LIG1
>> 0.0645
>> 56 H12 -2.2603 -0.6329 -1.8739 H 1 LIG1
>> 0.0645
>> 57 H13 -5.9324 -1.1833 -3.1491 H 1 LIG1
>> 0.1018
>> 58 H14 -1.3609 -4.8928 -0.3242 H 1 LIG1
>> 0.1064
>> 59 H15 -4.6910 -3.8437 2.3366 H 1 LIG1
>> 0.1259
>> 60 H16 -5.8375 -2.9879 1.5154 H 1 LIG1
>> 0.1259
>> 61 H17 -2.8150 4.6581 0.8568 H 1 LIG1
>> 0.0659
>> 62 H18 -2.1232 6.8857 1.5028 H 1 LIG1
>> 0.0675
>> 63 H19 0.5295 6.4594 0.8618 H 1 LIG1
>> 0.0853
>> 64 H20 -3.5627 0.4623 -3.5840 H 1 LIG1
>> 0.0659
>> 65 H21 -4.9700 -0.8302 -5.0011 H 1 LIG1
>> 0.0675
>> 66 H22 -3.6913 -3.2429 -4.7274 H 1 LIG1
>> 0.0854
>> 67 H23 -3.4491 3.6578 2.8683 H 1 LIG1
>> 0.2107
>> 68 H24 -0.3142 7.1392 2.9619 H 1 LIG1
>> 0.2108
>> 69 H25 -3.3167 -0.4612 -6.8446 H 1 LIG1
>> 0.2108
>> 70 H26 -3.5789 1.5634 -5.6077 H 1 LIG1
>> 0.2107
>> @<TRIPOS>BOND
>> 1 1 45 1
>> 2 1 2 ar
>> 3 1 6 ar
>> 4 2 46 1
>> 5 2 3 ar
>> 6 3 47 1
>> 7 3 4 ar
>> 8 4 5 ar
>> 9 5 48 1
>> 10 5 6 ar
>> 11 6 7 1
>> 12 7 9 am
>> 13 7 8 2
>> 14 9 50 1
>> 15 9 49 1
>> 16 10 11 1
>> 17 10 37 1
>> 18 11 35 1
>> 19 11 51 1
>> 20 11 12 1
>> 21 12 53 1
>> 22 12 52 1
>> 23 12 13 1
>> 24 13 14 1
>> 25 14 17 1
>> 26 14 16 1
>> 27 14 15 1
>> 28 17 18 1
>> 29 18 21 1
>> 30 18 20 1
>> 31 18 19 1
>> 32 22 40 1
>> 33 22 23 1
>> 34 23 24 1
>> 35 23 54 1
>> 36 23 38 1
>> 37 24 21 1
>> 38 24 56 1
>> 39 24 55 1
>> 40 25 29 ar
>> 41 25 26 ar
>> 42 26 57 1
>> 43 26 27 ar
>> 44 27 28 ar
>> 45 28 30 ar
>> 46 29 33 ar
>> 47 29 28 ar
>> 48 30 31 ar
>> 49 31 58 1
>> 50 31 32 ar
>> 51 32 33 ar
>> 52 33 34 1
>> 53 34 60 1
>> 54 34 59 1
>> 55 35 36 1
>> 56 35 61 1
>> 57 35 41 1
>> 58 36 37 1
>> 59 36 62 1
>> 60 36 42 1
>> 61 37 4 1
>> 62 37 63 1
>> 63 38 64 1
>> 64 38 44 1
>> 65 38 39 1
>> 66 39 65 1
>> 67 39 43 1
>> 68 39 40 1
>> 69 40 27 1
>> 70 40 66 1
>> 71 41 67 1
>> 72 42 68 1
>> 73 43 69 1
>> 74 44 70 1
>> @<TRIPOS>SUBSTRUCTURE
>> 1 LIG1 1 GROUP 1 LIG 1
>>
>> ============================================================================
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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