JT-1: DTAB Surfactant CGenFF

[Jacqueline-teixeira]

Hi,

Could you tell me if this dihedral is foreseen in the potential of CGenFF? The head of this surfactant is a choline and the tail is a hydrocarbon.

362 321 318 318 NOT FOUND
NG3P0 CG324 CG321 CG321

270 321 318 318 NOT FOUND
HGP5 CG324 CG321 CG321

[Sulstice]

huh I will take a look on monday. @asukaorr Do you wanna run through your versions and I'll had the SMILES version one.

[Jacqueline-teixeira]

Thanks Sulstice,
Here this coordinate file.

51

NG3P0 6.10700 0.11200 -0.00500
CG324 4.79600 -0.60400 0.07400
CG321 3.53800 0.29200 -0.02600
CG321 2.26200 -0.55500 0.06700
CG321 1.00800 0.32200 -0.03100
CG321 -0.26600 -0.52600 0.06300
CG321 -1.52000 0.35100 -0.03500
CG334 6.26400 0.81400 -1.30100
CG334 6.26300 1.08200 1.10500
CG334 7.18600 -0.90000 0.10800
CG321 -2.79400 -0.49700 0.05900
CG321 -4.04800 0.38000 -0.03800
CG321 -5.32200 -0.46800 0.05600
CG321 -6.57500 0.40900 -0.04100
CG321 -7.84800 -0.44000 0.05300
CG331 -9.09900 0.43000 -0.04300
HGP5 4.73600 -1.16100 1.03800
HGP5 4.73700 -1.36000 -0.74300
HGA2 3.52400 0.83000 -0.99700
HGA2 3.52300 1.03000 0.80200
HGA2 2.25200 -1.09900 1.03800
HGA2 2.25300 -1.29900 -0.75900
HGA2 1.01500 0.86600 -1.00100
HGA2 1.01400 1.06600 0.79600
HGA2 -0.27400 -1.27000 -0.76400
HGA2 -0.27400 -1.07000 1.03400
HGA2 -1.51300 1.09500 0.79200
HGA2 -1.51200 0.89500 -1.00500
HGP5 7.27800 1.26600 -1.39000
HGP5 5.53900 1.64800 -1.40800
HGP5 6.12500 0.11400 -2.15500
HGP5 5.53800 1.91900 1.02500
HGP5 7.27700 1.54200 1.09400
HGP5 6.12300 0.58700 2.09200
HGP5 7.12300 -1.44900 1.07500
HGP5 7.12400 -1.64800 -0.71400
HGP5 8.19300 -0.42700 0.05700
HGA2 -2.80100 -1.04100 1.03000
HGA2 -2.80100 -1.24100 -0.76800
HGA2 -4.04000 1.12400 0.78900
HGA2 -4.04000 0.92400 -1.00900
HGA2 -5.32900 -1.21200 -0.77100
HGA2 -5.32900 -1.01200 1.02700
HGA2 -6.56800 1.15300 0.78600
HGA2 -6.56800 0.95300 -1.01200
HGA2 -7.86400 -1.18300 -0.77300
HGA2 -7.86400 -0.98300 1.02300
HGA3 -9.12000 1.16900 0.78500
HGA3 -10.00400 -0.21000 0.02800
HGA3 -9.12000 0.96900 -1.01500
BRGA1 9.99764 0.75575 -0.21806

[asukaorr]

Sure, can you provide the mol2 file?

…

On Sat, Jul 30, 2022 at 1:53 PM Sul ***@***.***> wrote: huh I will take a look on monday. @asukaorr <https://github.com/asukaorr> Do you wanna run through your versions and I'll had the SMILES version one. — Reply to this email directly, view it on GitHub <https://github.com/Sulstice/global-chem/discussions/198#discussioncomment-3287835>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMIBXYWV7MAVJLIBGMLKVS3VWVT2NANCNFSM55DR3GIA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[Jacqueline-teixeira]

Hi @asukaorr , thanks for reply.

51 0 0 0 0
SMALL
GASTEIGER

@ATOM
1 * 6.1070 0.1120 -0.0050 NG3P0 1 UNL1 0.0000
2 * 4.7960 -0.6040 0.0740 CG324 2 UNL2 0.0000
3 * 3.5380 0.2920 -0.0260 CG321 3 UNL3 0.0000
4 * 2.2620 -0.5550 0.0670 CG321 4 UNL4 0.0000
5 * 1.0080 0.3220 -0.0310 CG321 5 UNL5 0.0000
6 * -0.2660 -0.5260 0.0630 CG321 6 UNL6 0.0000
7 * -1.5200 0.3510 -0.0350 CG321 7 UNL7 0.0000
8 * 6.2640 0.8140 -1.3010 CG334 8 UNL8 0.0000
9 * 6.2630 1.0820 1.1050 CG334 9 UNL9 0.0000
10 * 7.1860 -0.9000 0.1080 CG334 10 UNL10 0.0000
11 * -2.7940 -0.4970 0.0590 CG321 11 UNL11 0.0000
12 * -4.0480 0.3800 -0.0380 CG321 12 UNL12 0.0000
13 * -5.3220 -0.4680 0.0560 CG321 13 UNL13 0.0000
14 * -6.5750 0.4090 -0.0410 CG321 14 UNL14 0.0000
15 * -7.8480 -0.4400 0.0530 CG321 15 UNL15 0.0000
16 * -9.0990 0.4300 -0.0430 CG331 16 UNL16 0.0000
17 * 4.7360 -1.1610 1.0380 HGP5 17 UNL17 0.0000
18 * 4.7370 -1.3600 -0.7430 HGP5 18 UNL18 0.0000
19 * 3.5240 0.8300 -0.9970 HGA2 19 UNL19 0.0000
20 * 3.5230 1.0300 0.8020 HGA2 20 UNL20 0.0000
21 * 2.2520 -1.0990 1.0380 HGA2 21 UNL21 0.0000
22 * 2.2530 -1.2990 -0.7590 HGA2 22 UNL22 0.0000
23 * 1.0150 0.8660 -1.0010 HGA2 23 UNL23 0.0000
24 * 1.0140 1.0660 0.7960 HGA2 24 UNL24 0.0000
25 * -0.2740 -1.2700 -0.7640 HGA2 25 UNL25 0.0000
26 * -0.2740 -1.0700 1.0340 HGA2 26 UNL26 0.0000
27 * -1.5130 1.0950 0.7920 HGA2 27 UNL27 0.0000
28 * -1.5120 0.8950 -1.0050 HGA2 28 UNL28 0.0000
29 * 7.2780 1.2660 -1.3900 HGP5 29 UNL29 0.0000
30 * 5.5390 1.6480 -1.4080 HGP5 30 UNL30 0.0000
31 * 6.1250 0.1140 -2.1550 HGP5 31 UNL31 0.0000
32 * 5.5380 1.9190 1.0250 HGP5 32 UNL32 0.0000
33 * 7.2770 1.5420 1.0940 HGP5 33 UNL33 0.0000
34 * 6.1230 0.5870 2.0920 HGP5 34 UNL34 0.0000
35 * 7.1230 -1.4490 1.0750 HGP5 35 UNL35 0.0000
36 * 7.1240 -1.6480 -0.7140 HGP5 36 UNL36 0.0000
37 * 8.1930 -0.4270 0.0570 HGP5 37 UNL37 0.0000
38 * -2.8010 -1.0410 1.0300 HGA2 38 UNL38 0.0000
39 * -2.8010 -1.2410 -0.7680 HGA2 39 UNL39 0.0000
40 * -4.0400 1.1240 0.7890 HGA2 40 UNL40 0.0000
41 * -4.0400 0.9240 -1.0090 HGA2 41 UNL41 0.0000
42 * -5.3290 -1.2120 -0.7710 HGA2 42 UNL42 0.0000
43 * -5.3290 -1.0120 1.0270 HGA2 43 UNL43 0.0000
44 * -6.5680 1.1530 0.7860 HGA2 44 UNL44 0.0000
45 * -6.5680 0.9530 -1.0120 HGA2 45 UNL45 0.0000
46 * -7.8640 -1.1830 -0.7730 HGA2 46 UNL46 0.0000
47 * -7.8640 -0.9830 1.0230 HGA2 47 UNL47 0.0000
48 * -9.1200 1.1690 0.7850 HGA3 48 UNL48 0.0000
49 * -10.0040 -0.2100 0.0280 HGA3 49 UNL49 0.0000
50 * -9.1200 0.9690 -1.0150 HGA3 50 UNL50 0.0000
51 * 9.9976 0.7558 -0.2181 BRGA1 51 UNL51 0.0000

[asukaorr]

Thanks @Jacqueline-teixeira.

One thing I noticed is that you have the Br- counter ion in the mol2 file. When using the CGenFF web server, you'll need to clean it out.

From the CGenFF program output, we can see that the charge and parameter penalty scores are 0 (see "param penalty=" and "charge penalty=" in the CGenFF program output, surfactant.str). So your molecule is well described in CGenFF.

surfactant.zip

[Sulstice]

@asukaorr We did pretty well for a surfactant. I wonder what our tolerance is for this type of functional group styles.