GROMACS version:gromacs-2024.3
GROMACS modification: No
I’ve been trying to create a PDB file with lipid information using rdKit, SMILE string, formula e.t.c. The PDB files are created, but trying to use them with the pdb2gmx command gives me an error
“Fatal error:
Atom H1 in residue PALM 0 was not found in rtp entry PALM with 49 atoms
while sorting atoms.”
Regarding missing atoms in the residue type, I have selected. I’ve tried determining residue types using different ways such as checking the lipids.rtp file for the residue type with all of my lipid’s atoms and determining the residue type from the lipids name e.g 9,16-dihydroxy-palmitic acid, would have the residue type PALM. Might someone have an idea what I might be doing wrong? How I can correctly select a residue type for a lipid and thus create the correct pdb file?
Part of the generated PDF file is as follows:
ATOM 1 O1 PALM L 1 7.202 0.799 -2.407 1.00 0.00 0 O
ATOM 2 C1 PALM L 1 7.362 0.296 -1.167 1.00 0.00 0 C
ATOM 3 C2 PALM L 1 6.836 -1.110 -1.058 1.00 0.00 0 C
ATOM 4 C3 PALM L 1 6.596 -1.546 0.388 1.00 0.00 0 C
ATOM 5 C4 PALM L 1 5.474 -0.793 1.114 1.00 0.00 0 C
ATOM 6 C5 PALM L 1 4.092 -1.009 0.495 1.00 0.00 0 C
ATOM 7 C6 PALM L 1 2.998 -0.346 1.336 1.00 0.00 0 C
ATOM 8 C7 PALM L 1 1.615 -0.555 0.716 1.00 0.00 0 C
ATOM 9 C8 PALM L 1 0.525 0.112 1.558 1.00 0.00 0 C
ATOM 10 C9 PALM L 1 -0.895 -0.165 1.052 1.00 0.00 0 C
ATOM 11 C10 PALM L 1 -1.192 0.479 -0.305 1.00 0.00 0 C
ATOM 12 C11 PALM L 1 -2.611 0.202 -0.812 1.00 0.00 0 C
ATOM 13 C12 PALM L 1 -3.701 0.869 0.030 1.00 0.00 0 C
ATOM 14 C13 PALM L 1 -5.086 0.660 -0.590 1.00 0.00 0 C
ATOM 15 C14 PALM L 1 -6.177 1.321 0.255 1.00 0.00 0 C
ATOM 16 C15 PALM L 1 -7.568 1.233 -0.375 1.00 0.00 0 C
ATOM 17 C16 PALM L 1 -8.102 -0.187 -0.474 1.00 0.00 0 C
ATOM 18 O2 PALM L 1 7.910 0.953 -0.300 1.00 0.00 0 O
ATOM 19 H1 PALM L 1 7.596 1.695 -2.351 1.00 0.00 0 H
ATOM 20 H2 PALM L 1 5.916 -1.198 -1.642 1.00 0.00 0 H
ATOM 21 H3 PALM L 1 7.585 -1.770 -1.511 1.00 0.00 0 H
ATOM 22 H4 PALM L 1 7.522 -1.423 0.962 1.00 0.00 0 H
ATOM 23 H5 PALM L 1 6.365 -2.618 0.396 1.00 0.00 0 H
ATOM 24 H6 PALM L 1 5.699 0.279 1.149 1.00 0.00 0 H
ATOM 25 H7 PALM L 1 5.456 -1.140 2.155 1.00 0.00 0 H
ATOM 26 H8 PALM L 1 3.889 -2.083 0.410 1.00 0.00 0 H
ATOM 27 H9 PALM L 1 4.064 -0.590 -0.518 1.00 0.00 0 H
ATOM 28 H10 PALM L 1 3.013 -0.762 2.351 1.00 0.00 0 H
ATOM 29 H11 PALM L 1 3.203 0.728 1.424 1.00 0.00 0 H
ATOM 30 H12 PALM L 1 1.612 -0.142 -0.299 1.00 0.00 0 H
ATOM 31 H13 PALM L 1 1.409 -1.629 0.632 1.00 0.00 0 H
ATOM 32 H14 PALM L 1 0.696 1.195 1.598 1.00 0.00 0 H
ATOM 33 H15 PALM L 1 0.595 -0.257 2.589 1.00 0.00 0 H
ATOM 34 H16 PALM L 1 -1.594 0.223 1.801 1.00 0.00 0 H
ATOM 35 H17 PALM L 1 -1.060 -1.247 0.993 1.00 0.00 0 H
ATOM 36 H18 PALM L 1 -0.493 0.092 -1.055 1.00 0.00 0 H
ATOM 37 H19 PALM L 1 -1.027 1.562 -0.247 1.00 0.00 0 H
ATOM 38 H20 PALM L 1 -2.783 -0.881 -0.852 1.00 0.00 0 H
ATOM 39 H21 PALM L 1 -2.682 0.571 -1.843 1.00 0.00 0 H
ATOM 40 H22 PALM L 1 -3.700 0.456 1.045 1.00 0.00 0 H
ATOM 41 H23 PALM L 1 -3.495 1.943 0.115 1.00 0.00 0 H
ATOM 42 H24 PALM L 1 -5.279 -0.414 -0.680 1.00 0.00 0 H
ATOM 43 H25 PALM L 1 -5.101 1.081 -1.603 1.00 0.00 0 H
ATOM 44 H26 PALM L 1 -5.930 2.381 0.394 1.00 0.00 0 H
ATOM 45 H27 PALM L 1 -6.196 0.868 1.254 1.00 0.00 0 H
ATOM 46 H28 PALM L 1 -7.556 1.689 -1.372 1.00 0.00 0 H
ATOM 47 H29 PALM L 1 -8.263 1.824 0.235 1.00 0.00 0 H
ATOM 48 H30 PALM L 1 -7.511 -0.791 -1.170 1.00 0.00 0 H
ATOM 49 H31 PALM L 1 -8.095 -0.679 0.504 1.00 0.00 0 H
ATOM 50 H32 PALM L 1 -9.134 -0.176 -0.840 1.00 0.00 0 H
TER 51 PALM L 1