Dear gmx users, I am trying to make a new isopeptide bond between Lys and Gly in VERSION 4.5.4. I did it in VERSION 4.0.5 but can not do it in this version of Gromacs (steps are the same).
*In PDB:* ... ATOM 1474 NZ LYN A 93 0.422 60.111 0.829 1.00 1.85 A N ... ATOM 1485 HZ1 LYN A 93 0.848 60.489 1.646 1.00 0.22 A H (only one HZ) Terminal GLY also can be involved to isopeptide bond: ATOM 3827 N GLY B 240 2.191 62.558 -0.381 1.00 1.85 B N ATOM 3828 CA GLY B 240 0.775 62.390 -0.063 1.00 2.17 B C ATOM 3829 C GLY B 240 0.323 60.961 -0.200 1.00 2.00 B C ATOM 3830 O GLY B 240 -0.097 60.559 -1.281 1.00 1.70 B O ATOM 3831 HN GLY B 240 2.551 62.033 -1.148 1.00 0.22 B H ATOM 3832 HA1 GLY B 240 0.209 62.976 -0.771 1.00 1.32 B H ATOM 3833 HA2 GLY B 240 0.599 62.684 0.961 1.00 1.32 B H In Pymol the is a connection (NZ of LYS93_domain_A – 0.13 nm – C of GLY240_domain_B). *I added: * *1) *to ffbonded.itp [ angletypes ] HP CT N 1 109.500 418.400 [ bondtypes ] etc. for ineptitude bond are already exist *2) *to specbond.dat LYS NZ 1 GLY C 1 0.13 LYQ GLQ GLQ the same as GLY (originally it should be CGLY, it is C-terminal) LYQ the same as LYN, but only with one HZ1 and [NZ N - 0.64977 17] (instead of NZ N3) *3) *Added LYQ and GLQ to the residuetype.dat (to aminoacids.dat in VERSION 4.0.5) *4) *Added to aminoacids.hdb: LYQ 7 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG 2 6 HG CG CB CD 2 6 HD CD CG CE 2 6 HE CE CD NZ 1 1 HZ NZ CE CD GLQ – same as GLY *After* pdb2gmx -f ubc7_94_t48_newgmx1.pdb -o processed.gro -water tip3p -chainsep interactive -ignh -rtpres There are no LYQ and GLQ topol.top (instead of it LYS with 3 HZ3 and CGLY) and no bond (residues are not connected after minimization). Force field: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) ___________________________________ In VERSION 4.0.5 first I changed names of residues according to Amber (Amber 99) specificity: LYS to LYP and LYN etc. And in specbond.dat it was: LYN NZ 1 GLY C 1 0.13 LYQ GLQ (it works ok) -- Sincerely, Yulian Gavrilov
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