[gmx-users] make a new bond in VERSION 4.5.4

[Justin A. Lemkul]

Yulian Gavrilov wrote:
> 
> 
> 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)
> 

The next test would be to change the residue names in the .pdb file to LYQ and 
GLQ and make your entry in specbond.dat read:

LYQ    NZ   1    GLQ    C     1   0.13      LYQ     GLQ

The renaming schemes for residues under different force fields is a new addition 
in 4.5, so that could be the hangup.  If you keep the names the same throughout 
the process, that should avoid any issues.  If that doesn't work, please report 
back.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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