[gmx-users] LINCS warnings and ligand topology

[MPI]

Dear Users,

I prepared  ligand topologies by two different methods, one with
Acpype and the other with Prodrg.

It is sad that independent simulations give the same (or similar)
numerous Lincs warnings and the system blew up at the end.

Errors look like

LINCS WARNING relative constraint deviation after LINCS:
rms 0.019243, max 0.893307 (between atoms 2073 and 2121)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2073   2121   90.0    0.1758   0.1844      0.0974
Wrote pdb files with previous and current coordinates


I was able to trace down errors that came mainly from the "bad" atom
indexed 2073, which is an Oxygen in a gro file like

131DRG     O3 2073   1.789   5.047   4.061

131DRG    H45 2121   1.701   5.076   4.032


I suspect  atom 2121 is a polar H and it should be deprotonated or
removed ??? or did I miss something ?  but the question is how to
prepare this ligand topology without causing LINCS warnings.

Please also see attached ligand coordinates. This ligand is called
Cholesterol-Sulfate.

Comments and suggestions are highly appreciated.

Thank you.

Dewey


##############
HETATM 3204  C65 DRG           -18.194 -41.205  44.427  1.00 24.75           C
HETATM 3205  C63 DRG           -18.216 -39.779  43.816  1.00 25.87           C
HETATM 3206  C69 DRG           -17.181 -39.768  42.670  1.00 27.16           C
HETATM 3207  C60 DRG           -19.659 -39.482  43.335  1.00 22.85           C
HETATM 3208  C57 DRG           -19.904 -38.288  42.360  1.00 23.27           C
HETATM 3209  C54 DRG           -21.331 -37.724  42.522  1.00 22.65           C
HETATM 3210  C48 DRG           -21.556 -36.728  43.707  1.00 21.56           C
HETATM 3211  C50 DRG           -20.949 -35.357  43.312  1.00 21.66           C
HETATM 3212  C38 DRG           -23.088 -36.562  43.980  1.00 19.68           C
HETATM 3213  C35 DRG           -23.755 -37.943  44.393  1.00 19.33           C
HETATM 3214  C29 DRG           -23.647 -35.601  45.119  1.00 20.43           C
HETATM 3215  C26 DRG           -23.672 -34.063  44.861  1.00 18.19           C
HETATM 3216  C40 DRG           -22.855 -35.867  46.471  1.00 19.33           C
HETATM 3217  C30 DRG           -25.126 -36.065  45.109  1.00 20.16           C
HETATM 3218  C32 DRG           -25.089 -37.602  45.149  1.00 21.12           C
HETATM 3219  C18 DRG           -25.966 -35.363  46.270  1.00 20.54           C
HETATM 3220  C15 DRG           -27.466 -35.864  46.269  1.00 20.53           C
HETATM 3221  C20 DRG           -25.882 -33.782  46.078  1.00 19.48           C
HETATM 3222  C23 DRG           -24.368 -33.295  46.033  1.00 18.16           C
HETATM 3223  C22 DRG           -26.738 -33.026  47.187  1.00 20.09           C
HETATM 3224  C44 DRG           -25.993 -33.014  48.578  1.00 20.12           C
HETATM 3225  C12 DRG           -28.142 -33.677  47.356  1.00 21.29           C
HETATM 3226  C9  DRG           -29.244 -32.840  48.027  1.00 22.75           C
HETATM 3227  C13 DRG           -28.452 -34.928  46.949  1.00 21.74           C
HETATM 3228  C1  DRG           -26.966 -31.552  46.696  1.00 21.36           C
HETATM 3229  C4  DRG           -27.873 -30.736  47.660  1.00 24.07           C
HETATM 3230  C7  DRG           -29.286 -31.360  47.578  1.00 25.09           C
HETATM 3231  O6  DRG           -30.237 -30.768  48.473  1.00 27.57           O
HETATM 3232  S1  DRG           -31.603 -30.323  48.000  1.00 29.68           S
HETATM 3233  O3  DRG           -32.343 -29.771  49.139  1.00 30.75           O
HETATM 3234  O2  DRG           -32.314 -31.418  47.371  1.00 27.84           O
HETATM 3235  O4  DRG           -31.343 -29.261  47.002  1.00 27.97           O