[gmx-users] question

[Justin Lemkul]

On 5/12/15 11:55 PM, Andrew Bostick wrote:
> Dear Justin
>
> Since I want to consider the special bond between CD atom of GLU residue
> form peptide 1 and NZ atom of LYS residue from peptide 2, I did following
> steps:
>
> 1) I created 1 pdb file containing 2 peptides without any connection
> between aformentioned atoms (CD & NZ). I deleted OE2 atom of GLU residue
> and HZ2 and HZ3 atoms of LYS residue.
>
> 2) I created a new entry in specbond.dat and two .rtp entries in gromos
> 43a1.ff. These are as follows:
>
> In specbond.dat file:
> GLU     CD      1       LYS     NZ      1       0.13    GLU2    LYS2
>
> In aminoacids.rtp file:
> [ 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
>    HZ1     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   HZ1    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   HZ1     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   HZ1     gd_14
> ----------------------------------------------
>
> [ 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
>    OE1    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   OE1    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   OE1     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
>
> After using pdb2gmx, I encountered with:
>
> WARNING: atom OE2 is missing in residue Glu 417 in the pdb file.
>
> What is wrong in my steps?
>

This implies that the two residues you want bonded together to form the 
isopeptide bond do not satisfy the distance criterion in specbond.dat, so they 
don't get renamed and the wrong .rtp entries are processed.  The screen output 
of pdb2gmx (in which it prints the special bond distance matrix) would be 
definitive.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================