Custom Search
-- Gustavo Seabra. ________________________________ From: Enrico Martinez via AMBER <amber.ambermd.org> Sent: Thursday, November 24, 2022 10:51:11 AM To: AMBER Mailing List <amber.ambermd.org> Subject: [AMBER] Applying position restraint on ligand Dear Amber Users, Currently I am performing equilibration of my protein-ligand system using the following amber mask used to freeze all backbone atoms of protein excluding water residues (containing O atom) restraintmask='(.CA,CA,N,O & !:WAT)' Using this selection, I would like to add selected atom of the ligand (residue "lig") e.g. to apply position restraints on the atom C1. Here is the PDB format of the ligand present in the same model: ATOM 9275 N lig 608 -7.093 -20.714 4.036 1.00 0.00 ATOM 9276 N1 lig 608 -6.438 -17.078 3.587 1.00 0.00 ATOM 9277 N2 lig 608 -8.410 -24.956 0.057 1.00 0.00 ATOM 9278 N3 lig 608 -6.296 -24.226 -0.519 1.00 0.00 ATOM 9279 N4 lig 608 -9.281 -23.257 11.747 1.00 0.00 ATOM 9280 C lig 608 -4.815 -25.159 7.597 1.00 0.00 ATOM 9281 C1 lig 608 -5.456 -24.863 8.800 1.00 0.00 ATOM 9282 C2 lig 608 -6.465 -23.902 8.829 1.00 0.00 ATOM 9283 C3 lig 608 -6.793 -23.211 7.658 1.00 0.00 ATOM 9284 C4 lig 608 -6.145 -23.506 6.451 1.00 0.00 ATOM 9285 C5 lig 608 -5.159 -24.496 6.422 1.00 0.00 ATOM 9286 C6 lig 608 -6.493 -22.779 5.220 1.00 0.00 ATOM 9287 C7 lig 608 -6.641 -21.287 5.234 1.00 0.00 ATOM 9288 C8 lig 608 -6.682 -23.457 4.077 1.00 0.00 ATOM 9289 C9 lig 608 -7.285 -21.470 2.886 1.00 0.00 ATOM 9290 C10 lig 608 -7.052 -22.793 2.837 1.00 0.00 ATOM 9291 C11 lig 608 -7.305 -19.306 4.000 1.00 0.00 ATOM 9292 C12 lig 608 -8.576 -18.774 4.226 1.00 0.00 ATOM 9293 C13 lig 608 -6.272 -18.418 3.711 1.00 0.00 ATOM 9294 C14 lig 608 -8.763 -17.395 4.159 1.00 0.00 ATOM 9295 C15 lig 608 -7.679 -16.600 3.824 1.00 0.00 ATOM 9296 C16 lig 608 -7.165 -23.504 1.566 1.00 0.00 ATOM 9297 C17 lig 608 -8.393 -24.307 1.260 1.00 0.00 ATOM 9298 C18 lig 608 -6.185 -23.519 0.646 1.00 0.00 ATOM 9299 C19 lig 608 -7.391 -24.975 -0.850 1.00 0.00 ATOM 9300 C20 lig 608 -8.007 -22.375 9.811 1.00 0.00 ATOM 9301 C21 lig 608 -9.283 -22.478 10.593 1.00 0.00 ATOM 9302 C22 lig 608 -10.498 -21.874 10.307 1.00 0.00 ATOM 9303 C23 lig 608 -10.458 -23.196 12.328 1.00 0.00 ATOM 9304 C24 lig 608 -10.887 -20.992 9.174 1.00 0.00 ATOM 9305 O lig 608 -6.405 -20.658 6.265 1.00 0.00 ATOM 9306 O1 lig 608 -9.335 -24.385 2.045 1.00 0.00 ATOM 9307 O2 lig 608 -7.445 -25.622 -1.888 1.00 0.00 ATOM 9308 O3 lig 608 -7.163 -23.529 9.947 1.00 0.00 ATOM 9309 Cl lig 608 -3.583 -26.361 7.561 1.00 0.00 ATOM 9310 S lig 608 -11.642 -22.255 11.530 1.00 0.00 Could you please suggest to me how the restraint mask indicated above could be modified in order to freeze ligands at one point of the atom C1? Many thanks in advance! Cheers, Enrico _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Nov 24 2022 - 08:30:02 PST