Hi again,
I sent a BSM job with a protein receptor and a SMALL non peptide ligand (histamine) whose sdf file is below. Got the same error message :
An error found in the submitted ligand strucutre.
Please check if the ligand has correct file format and chemical structure.
SDF file :
HME_marvin_vmd
3D
Structure written by MMmdl.
18 18 0 0 1 0 999 V2000
1.1520 -0.5180 4.3930 N 0 0 0 0 0 0
0.0860 -1.3160 4.2480 C 0 0 3 0 0 0
-0.5620 -1.0130 3.1100 N 0 0 0 0 0 0
0.1170 -0.0090 2.5260 C 0 0 3 0 0 0
1.2000 0.3060 3.3430 C 0 0 3 0 0 0
-0.2210 0.6130 1.2320 C 0 0 0 0 0 0
0.4820 -0.1150 0.0630 C 0 0 0 0 0 0
0.1540 0.5190 -1.2180 N 0 0 0 0 0 0
1.7840 -0.5390 5.1300 H 0 0 0 0 0 0
-0.1890 -2.0500 4.9020 H 0 0 0 0 0 0
1.9070 1.0270 3.1740 H 0 0 0 0 0 0
0.0770 1.6650 1.2400 H 0 0 0 0 0 0
-1.3030 0.5710 1.0850 H 0 0 0 0 0 0
0.1650 -1.1610 0.0190 H 0 0 0 0 0 0
1.5660 -0.0800 0.1930 H 0 0 0 0 0 0
-0.8570 0.4830 -1.3690 H 0 0 0 0 0 0
0.4630 1.4930 -1.2040 H 0 0 0 0 0 0
0.6280 0.0230 -1.9770 H 0 0 0 0 0 0
1 2 1 0 0 0
1 5 1 0 0 0
1 9 1 0 0 0
2 3 1 0 0 0
2 10 1 0 0 0
3 4 1 0 0 0
4 5 1 0 0 0
4 6 1 0 0 0
5 11 1 0 0 0
6 7 1 0 0 0
6 12 1 0 0 0
6 13 1 0 0 0
7 8 1 0 0 0
7 14 1 0 0 0
7 15 1 0 0 0
8 16 1 0 0 0
8 17 1 0 0 0
8 18 1 0 0 0
M END
>
HME_marvin_vmd.1
>
0
>
0
>
0
>
90
>
90
>
90
>
P 1
>
1
>
18
$$$$