[gmx-users] question

[Andrew Bostick]

Dear Justin

I was really confused. I know that my peroblem is in incorrect entries
(LYS2 and GLU2) in aminoacids.rtp file

Sinse I want to have a isopeptide bond between (CD atom of GLU residue
from chain B and NZ atom of LYS residue from chain E), thus I should
use one HZ atom (for LYS2) and one OE atom (for GLU2) as follows. Is my
vision true?

[ GLU2 ]
 [ atoms ]
    N     N    -0.28000     0
    H     H     0.28000     0
   CA   CH1     0.00000     1
   CB   CH2     0.00000     1
   CG   CH2     0.00000     1
   CD     C     0.50000     2
   OE    OM    -0.50000     2
    C     C       0.380     3
    O     O      -0.380     3
 [ bonds ]
    N     H    gb_2
    N    CA    gb_20
   CA     C    gb_26
    C     O    gb_4
    C    +N    gb_9
   CA    CB    gb_26
   CB    CG    gb_26
   CG    CD    gb_26
   CD    OE    gb_5
 [ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_31
    H     N    CA     ga_17
   -C     N    CA     ga_30
    N    CA     C     ga_12
   CA     C    +N     ga_18
   CA     C     O     ga_29
    O     C    +N     ga_32
    N    CA    CB     ga_12
    C    CA    CB     ga_12
   CA    CB    CG     ga_14
   CB    CG    CD     ga_14
   CG    CD    OE     ga_21
 [ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1
    C    CA    +N     O     gi_1
   CA     N     C    CB     gi_2
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_4
   -C     N    CA     C     gd_19
    N    CA     C    +N     gd_20
    N    CA    CB    CG     gd_17
   CA    CB    CG    CD     gd_17


[ LYS2 ]
 [ atoms ]
    N     N    -0.28000     0
    H     H     0.28000     0
   CA   CH1     0.00000     1
   CB   CH2     0.00000     1
   CG   CH2     0.00000     2
   CD   CH2     0.00000     2
   CE   CH2     0.00000     3
   NZ    NT    -0.50000     3
   HZ     H     0.50000     3
    C     C       0.380     4
    O     O      -0.380     4
 [ bonds ]
    N     H    gb_2
    N    CA    gb_20
   CA     C    gb_26
    C     O    gb_4
    C    +N    gb_9
   CA    CB    gb_26
   CB    CG    gb_26
   CG    CD    gb_26
   CD    CE    gb_26
   CE    NZ    gb_20
   NZ    HZ    gb_2
 [ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_31
    H     N    CA     ga_17
   -C     N    CA     ga_30
    N    CA     C     ga_12
   CA     C    +N     ga_18
   CA     C     O     ga_29
    O     C    +N     ga_32
    N    CA    CB     ga_12
    C    CA    CB     ga_12
   CA    CB    CG     ga_14
   CB    CG    CD     ga_14
   CG    CD    CE     ga_14
   CD    CE    NZ     ga_14
   CE    NZ    HZ     ga_10
 [ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1
    C    CA    +N     O     gi_1
   CA     N     C    CB     gi_2
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_4
   -C     N    CA     C     gd_19
    N    CA     C    +N     gd_20
    N    CA    CB    CG     gd_17
   CA    CB    CG    CD     gd_17
   CB    CG    CD    CE     gd_17
   CG    CD    CE    NZ     gd_17
   CD    CE    NZ    HZ     gd_14
----------------------------------------------------------------------------
Unfortunately, after using pdb2gmx, I encountered with:

Linking CYS-252 SG-248 and CYS-312 SG-743...
Linking CYS-358 SG-1094 and CYS-416 SG-1565...
Linking GLU-380 CD-1269 and LYS-540 NZ-2499...
Start terminus PRO-220: PRO-NH2+
End terminus HIS-434: COO-
Start terminus GLY-435: GLY-NH3+
End terminus LYS-551: COO-

-------------------------------------------------------
Program gmx, VERSION 5.0.5
Source code file:
/export/apps/gromacs/gromacs-5.0.5/src/gromacs/gmxpreprocess/pdb2gmx.c,
line: 732

Fatal error:
Atom OE1 in residue GLU 380 was not found in rtp entry GLU2 with 9
atoms while sorting atoms.
-------------------------------------------------------

I made GLU2 and LYS2 based on isopeptide bond, what is the resaon of this
error?

Thanks in advance.