Dear AMBER users,
Greetings!
I am planning to run a protein-Lipid bilayer simulation. My protein
contains standard residues, organic and metal cofactors (after correct
protonation ~45000 atoms)
I followed these steps in order to prepare the PDB for the lipid bilayer
simulations:
1. I used the CHARMM-GUI server to create a 175X175 Ang^2 POPC patch along
with the water ~20angs above the Z-axis and later converting to AMBER
format using *charmmlipid2amber.py* script.
2. Assemble the membrane+protein+cofactors in a single PDB and then
renumber using the pdb4amber program. (now total 441814 Atoms)
The pdb4amber renumbered my POPC into something like this:
HETATM63112 H18T OL 3605 -26.878 61.794 2.570 1.00 0.00
H
TER 63112 OL 3605
HETATM63113 C12 PA 3606 -16.857 66.773 15.532 1.00 0.00
C
HETATM63114 H2R PA 3606 -15.963 67.403 15.730 1.00 0.00
H
HETATM63115 H2S PA 3606 -17.622 67.168 16.235 1.00 0.00
H
HETATM63116 C13 PA 3606 -17.468 67.127 14.152 1.00 0.00
C
HETATM63117 H3R PA 3606 -17.955 68.124 14.101 1.00 0.00
H
HETATM63118 H3S PA 3606 -18.325 66.425 14.068 1.00 0.00
H
HETATM63119 C14 PA 3606 -16.514 67.122 12.902 1.00 0.00
C
HETATM63120 H4R PA 3606 -15.877 66.214 12.847 1.00 0.00
H
HETATM63121 H4S PA 3606 -15.866 68.024 12.923 1.00 0.00
H
HETATM63122 C15 PA 3606 -17.199 67.326 11.567 1.00 0.00
C
HETATM63123 H5R PA 3606 -17.752 68.289 11.529 1.00 0.00
H
HETATM63124 H5S PA 3606 -18.017 66.574 11.544 1.00 0.00
H
HETATM63125 C16 PA 3606 -16.284 67.133 10.328 1.00 0.00
C
HETATM63126 H6R PA 3606 -15.513 66.334 10.286 1.00 0.00
H
HETATM63127 H6S PA 3606 -15.628 68.027 10.396 1.00 0.00
H
HETATM63128 C17 PA 3606 -17.059 67.202 8.999 1.00 0.00
C
HETATM63129 H7R PA 3606 -17.399 68.244 8.815 1.00 0.00
H
HETATM63130 H7S PA 3606 -17.971 66.589 9.163 1.00 0.00
H
HETATM63131 C18 PA 3606 -16.362 66.819 7.679 1.00 0.00
C
HETATM63132 H8R PA 3606 -16.134 65.732 7.634 1.00 0.00
H
HETATM63133 H8S PA 3606 -15.342 67.255 7.744 1.00 0.00
H
HETATM63134 C19 PA 3606 -17.049 67.249 6.390 1.00 0.00
C
HETATM63135 H9R PA 3606 -17.257 68.333 6.517 1.00 0.00
H
HETATM63136 H9S PA 3606 -18.098 66.886 6.446 1.00 0.00
H
HETATM63137 C110 PA 3606 -16.461 66.758 5.029 1.00 0.00
C
HETATM63138 H10R PA 3606 -17.032 67.218 4.194 1.00 0.00
H
HETATM63139 H10S PA 3606 -16.705 65.675 4.981 1.00 0.00
H
HETATM63140 C111 PA 3606 -14.968 67.055 4.870 1.00 0.00
C
HETATM63141 H11R PA 3606 -14.439 66.441 5.631 1.00 0.00
H
HETATM63142 H11S PA 3606 -14.972 68.135 5.131 1.00 0.00
H
HETATM63143 C112 PA 3606 -14.403 66.708 3.487 1.00 0.00
C
HETATM63144 H12R PA 3606 -14.813 67.343 2.673 1.00 0.00
H
HETATM63145 H12S PA 3606 -14.620 65.632 3.313 1.00 0.00
H
HETATM63146 C113 PA 3606 -12.874 66.957 3.484 1.00 0.00
C
HETATM63147 H13R PA 3606 -12.474 66.407 4.362 1.00 0.00
H
HETATM63148 H13S PA 3606 -12.723 68.058 3.461 1.00 0.00
H
HETATM63149 C114 PA 3606 -12.301 66.473 2.189 1.00 0.00
C
HETATM63150 H14R PA 3606 -11.481 67.169 1.912 1.00 0.00
H
HETATM63151 H14S PA 3606 -13.052 66.543 1.374 1.00 0.00
H
HETATM63152 C115 PA 3606 -11.778 64.991 2.306 1.00 0.00
C
HETATM63153 H15R PA 3606 -12.682 64.386 2.527 1.00 0.00
H
HETATM63154 H15S PA 3606 -11.080 64.991 3.170 1.00 0.00
H
HETATM63155 C116 PA 3606 -10.945 64.570 1.109 1.00 0.00
C
HETATM63156 H16R PA 3606 -10.047 65.212 0.987 1.00 0.00
H
HETATM63157 H16S PA 3606 -11.593 64.814 0.240 1.00 0.00
H
HETATM63158 H16T PA 3606 -10.617 63.509 1.080 1.00 0.00
H
HETATM63159 N31 PC 3607 -10.535 69.653 19.930 1.00 0.00
N
HETATM63160 C32 PC 3607 -11.481 68.755 20.720 1.00 0.00
C
HETATM63161 H2A PC 3607 -11.677 69.215 21.678 1.00 0.00
H
HETATM63162 H2B PC 3607 -10.945 67.830 20.875 1.00 0.00
H
HETATM63163 C33 PC 3607 -11.210 70.854 19.303 1.00 0.00
C
HETATM63164 H3A PC 3607 -12.063 70.556 18.712 1.00 0.00
H
HETATM63165 H3B PC 3607 -11.572 71.386 20.170 1.00 0.00
H
HETATM63166 H3C PC 3607 -10.447 71.399 18.767 1.00 0.00
H
HETATM63167 C34 PC 3607 -9.393 70.091 20.862 1.00 0.00
C
HETATM63168 H4A PC 3607 -8.901 69.237 21.302 1.00 0.00
H
HETATM63169 H4B PC 3607 -8.719 70.669 20.247 1.00 0.00
H
HETATM63170 H4C PC 3607 -9.797 70.729 21.635 1.00 0.00
H
HETATM63171 C35 PC 3607 -9.986 68.888 18.781 1.00 0.00
C
HETATM63172 H5A PC 3607 -10.783 68.323 18.320 1.00 0.00
H
HETATM63173 H5B PC 3607 -9.310 68.170 19.220 1.00 0.00
H
HETATM63174 H5C PC 3607 -9.413 69.594 18.197 1.00 0.00
H
HETATM63175 C31 PC 3607 -12.879 68.362 20.065 1.00 0.00
C
HETATM63176 H1A PC 3607 -13.501 69.272 19.930 1.00 0.00
H
HETATM63177 H1B PC 3607 -13.490 67.653 20.663 1.00 0.00
H
HETATM63178 P31 PC 3607 -13.844 67.571 17.790 1.00 0.00
P
HETATM63179 O33 PC 3607 -13.302 67.343 16.411 1.00 0.00
O
HETATM63180 O34 PC 3607 -14.804 68.579 18.027 1.00 0.00
O
HETATM63181 O32 PC 3607 -12.700 67.807 18.839 1.00 0.00
O
HETATM63182 O31 PC 3607 -14.464 66.213 18.272 1.00 0.00
O
HETATM63183 C3 PC 3607 -13.750 64.962 18.368 1.00 0.00
C
HETATM63184 HA PC 3607 -14.051 64.602 19.375 1.00 0.00
H
HETATM63185 HB PC 3607 -12.652 65.129 18.336 1.00 0.00
H
HETATM63186 C2 PC 3607 -14.129 63.907 17.253 1.00 0.00
C
HETATM63187 HX PC 3607 -13.678 62.937 17.552 1.00 0.00
H
HETATM63188 O21 PC 3607 -13.636 64.401 15.918 1.00 0.00
O
HETATM63189 C21 PC 3607 -12.327 64.247 15.804 1.00 0.00
C
HETATM63190 O22 PC 3607 -11.598 63.541 16.467 1.00 0.00
O
HETATM63191 C1 PC 3607 -15.705 63.649 17.188 1.00 0.00
C
HETATM63192 HR PC 3607 -16.148 63.247 18.124 1.00 0.00
H
HETATM63193 HS PC 3607 -15.913 62.902 16.393 1.00 0.00
H
HETATM63194 O11 PC 3607 -16.483 64.886 16.936 1.00 0.00
O
HETATM63195 C11 PC 3607 -16.541 65.293 15.670 1.00 0.00
C
HETATM63196 O12 PC 3607 -16.257 64.553 14.751 1.00 0.00
O
HETATM63197 C12 OL 3608 -11.828 65.062 14.573 1.00 0.00
C
HETATM63198 H2R OL 3608 -12.615 65.801 14.310 1.00 0.00
H
HETATM63199 H2S OL 3608 -11.703 64.384 13.702 1.00 0.00
H
HETATM63200 C13 OL 3608 -10.623 65.709 15.027 1.00 0.00
C
HETATM63201 H3R OL 3608 -9.861 65.188 15.646 1.00 0.00
H
HETATM63202 H3S OL 3608 -10.990 66.515 15.698 1.00 0.00
H
HETATM63203 C14 OL 3608 -9.864 66.562 13.921 1.00 0.00
C
HETATM63204 H4R OL 3608 -9.359 65.849 13.234 1.00 0.00
H
HETATM63205 H4S OL 3608 -9.102 67.082 14.540 1.00 0.00
H
HETATM63206 C15 OL 3608 -10.706 67.537 13.126 1.00 0.00
C
HETATM63207 H5R OL 3608 -10.086 68.447 12.981 1.00 0.00
H
HETATM63208 H5S OL 3608 -11.579 67.725 13.786 1.00 0.00
H
HETATM63209 C16 OL 3608 -11.091 66.933 11.749 1.00 0.00
C
HETATM63210 H6R OL 3608 -11.507 65.915 11.903 1.00 0.00
H
HETATM63211 H6S OL 3608 -10.144 66.826 11.177 1.00 0.00
H
HETATM63212 C17 OL 3608 -12.240 67.665 10.923 1.00 0.00
C
HETATM63213 H7R OL 3608 -13.091 67.686 11.637 1.00 0.00
H
HETATM63214 H7S OL 3608 -12.376 66.964 10.072 1.00 0.00
H
HETATM63215 C18 OL 3608 -11.848 69.091 10.333 1.00 0.00
C
HETATM63216 H8R OL 3608 -10.821 69.025 9.914 1.00 0.00
H
HETATM63217 H8S OL 3608 -11.824 69.845 11.149 1.00 0.00
H
HETATM63218 C19 OL 3608 -12.860 69.581 9.260 1.00 0.00
C
HETATM63219 H9R OL 3608 -13.899 69.297 9.480 1.00 0.00
H
HETATM63220 C110 OL 3608 -12.576 70.400 8.181 1.00 0.00
C
HETATM63221 H10R OL 3608 -13.399 70.741 7.536 1.00 0.00
H
HETATM63222 C111 OL 3608 -11.185 70.900 7.816 1.00 0.00
C
HETATM63223 H11R OL 3608 -10.486 70.580 8.617 1.00 0.00
H
HETATM63224 H11S OL 3608 -11.171 72.010 7.842 1.00 0.00
H
HETATM63225 C112 OL 3608 -10.661 70.364 6.509 1.00 0.00
C
HETATM63226 H12R OL 3608 -9.707 70.925 6.408 1.00 0.00
H
HETATM63227 H12S OL 3608 -11.233 70.810 5.668 1.00 0.00
H
HETATM63228 C113 OL 3608 -10.319 68.898 6.406 1.00 0.00
C
HETATM63229 H13R OL 3608 -11.255 68.332 6.212 1.00 0.00
H
HETATM63230 H13S OL 3608 -9.983 68.516 7.394 1.00 0.00
H
HETATM63231 C114 OL 3608 -9.294 68.404 5.450 1.00 0.00
C
HETATM63232 H14R OL 3608 -9.282 67.294 5.398 1.00 0.00
H
HETATM63233 H14S OL 3608 -8.307 68.698 5.867 1.00 0.00
H
HETATM63234 C115 OL 3608 -9.450 68.918 4.082 1.00 0.00
C
HETATM63235 H15R OL 3608 -9.181 69.995 4.034 1.00 0.00
H
HETATM63236 H15S OL 3608 -10.550 68.961 3.936 1.00 0.00
H
HETATM63237 C116 OL 3608 -8.674 68.210 2.935 1.00 0.00
C
HETATM63238 H16R OL 3608 -8.940 67.132 2.898 1.00 0.00
H
HETATM63239 H16S OL 3608 -7.589 68.261 3.169 1.00 0.00
H
HETATM63240 C117 OL 3608 -8.888 68.721 1.462 1.00 0.00
C
HETATM63241 H17R OL 3608 -9.973 68.720 1.220 1.00 0.00
H
HETATM63242 H17S OL 3608 -8.297 68.094 0.761 1.00 0.00
H
HETATM63243 C118 OL 3608 -8.375 70.221 1.290 1.00 0.00
C
HETATM63244 H18R OL 3608 -8.534 70.559 0.243 1.00 0.00
H
HETATM63245 H18S OL 3608 -7.321 70.234 1.641 1.00 0.00
H
HETATM63246 H18T OL 3608 -8.922 70.960 1.914 1.00 0.00
H
TER 63246 OL 3608
HETATM63247 C12 PA 3609 76.573 3.217 11.778 1.00 0.00
C
As you can see the residue numbering of the head and the tail groups (for
PA, PC and OL) are different, in principle, these must possess the same
number for the application of the lipid17 FF. I do not see, currently, any
alternative to this approach for creating the PDB for tleap. Any help
would be appreciated.
In addition, pdb4amber again starts renumbering water from 1 (or any other
number) once the residue limit of 9999 is reached. (which implies there are
many waters sharing the same name, is this OK normally in such cases??) For
e.g.
HETATM23167 O WAT 99998 -54.270 -11.273 80.492 1.00 0.00
O
HETATM23168 H1 WAT 99998 -54.973 -10.658 80.282 1.00 0.00
H
HETATM23169 H2 WAT 99998 -54.715 -12.110 80.623 1.00 0.00
H
HETATM23170 O WAT 09 -67.022 4.490 80.038 1.00 0.00
O
HETATM23171 H1 WAT 09 -67.707 4.452 79.371 1.00 0.00
H
HETATM23172 H2 WAT 09 -67.018 5.403 80.327 1.00 0.00
H
I also used PACKMOL-MEMGEN for creating the protein-bilayer system. It
assigned chain ID to residues after noticing 9999 residues (message in
PACKMOL:Warning: There will be more than 9999 molecules of type 4
Residue numbering is reset after 9999.
Each set be will be assigned a different chain in the PDB output file.).
for e.g.
ATOM ***** O WAT I9999 60.735 -39.516 54.104 1.00 0.00
TIP3
ATOM ***** H1 WAT I9999 60.611 -39.191 54.997 1.00 0.00
TIP3
ATOM ***** H2 WAT I9999 61.651 -39.328 53.904 1.00 0.00
TIP3
TER
ATOM ***** O WAT J 1 -19.222 74.676 61.458 1.00 0.00
TIP3
ATOM ***** H1 WAT J 1 -18.307 74.661 61.174 1.00 0.00
TIP3
ATOM ***** H2 WAT J 1 -19.688 74.176 60.789 1.00 0.00
TIP3
Can I use this PDB with the chain IDs into tleap, despite the fact that it
is not pdb4amber'ed. In case I usepdb4amber again, I am stuck again with
the problem mentioned before (see point 2).
I would like to know how experts handle such protein with co-factors, lipid
bilayer, >9999 residues etc etc..
Cheers
Abhishek
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Received on Mon May 27 2019 - 10:00:02 PDT
