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

[Yulian Gavrilov]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110705/07fe4dd9/attachment.html>