[gmx-users] lactam bridge problems

Tue Feb 1 19:46:36 CET 2011

I want to create a peptide bond between glu and lys using Gromacs 4.5.3. One option that I have is to modify the topology file (bonds, angles, etc.) but I also want to do a number of these lactam bridges so it is a pain to make the bonds, delete the atoms in glu and lys that are not needed and renumber the .itp and .gro files. 

The other option is to add the lactam glu (LCE) and lactam lys (LCK) as residues to the force field. So far I have added LCE and LCK to gromos53a6 and opls-aa but i always get the same error: "Atom HZ1 not found in rtp database in residue LCK, it looks a bit like HZ" - there is no HZ1 in all my files but pdb2gmx seem to be looking for it.

The naming is consistent (HZ is specified in the .rtp files, in the pdb file). Here are the modiifcation that I made involving gromos53a6. 

Following the "Adding a residue to a
 force field section" in the gromacs website
1.)
-------- In aminoacids.rtp (I'm just showing LCK)
[ LCK ]
 [ atoms ]
    N     N    -0.31000     0
    H     H     0.31000     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     N    -0.31000     3 ; same atom type as amide N
   HZ
     H     0.31000     3 ; same atom type as amide H
    C     C       0.450     4
    O     O      -0.450     4
 [ bonds ]
    N     H    gb_2
    N    CA    gb_21
   CA    CB    gb_27
   CA     C    gb_27
   CB    CG    gb_27
   CG    CD    gb_27
   CD    CE    gb_27
   CE    NZ    gb_21 ; same bond as N-CA
   NZ    HZ    gb_2 ; same bond
 as N-H
    C     O    gb_5
    C    +N    gb_10
 [ angles ] 
;  ai    aj    ak   gromos type
   -C     N     H     ga_32
   -C     N    CA     ga_31
    H     N    CA     ga_18
    N    CA    CB     ga_13
    N    CA     C     ga_13
   CB    CA     C     ga_13
   CA    CB    CG     ga_15

 CB    CG    CD     ga_15
   CG    CD    CE     ga_15
   CD    CE    NJ     ga_15
   CE    NJ    HJ     ga_31
   CA     C     O     ga_30
   CA     C    +N     ga_19
    O     C    +N     ga_33
 [ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1
   CA     N    
 C    CB     gi_2
    C    CA    +N     O     gi_1
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_14
   -C     N    CA     C     gd_39
    N    CA    CB    CG     gd_34
    N    CA     C    +N     gd_40
   CA    CB    CG    CD     gd_34
   CB    CG    CD   
 CE     gd_34
   CG    CD    CE    NJ     gd_34
   CD    CE    NJ    HJ     gd_29

2.) HBD has been update 
LCK     2
1       1       H       N       -C      CA
2       4       HZ      NZ      CE      CD

3.) no new atom types introduced atomtypes.atp and ffnonbonded.itp not modified. Note: I did try introducing new atom types in a previous attempt (not on this attempt) but I still get the same error above.    

4.) no new bond types introduced (ffbonded.itp is
 not modified). 

5.) In residuetypes.dat (the new residues were declared)
LCK     Protein
LCE     Protein 

6.) specbond.dat (the peptide bond was introduced)
LCE     CD      1       LCK     NZ      1       0.133   LCTM    LCTM

It seems like pdb2gmx is still looking at my new residues as if they were lys and glu and that might be the source of the error (In my original pdb file, LCE and LCK were used so the error does not come from there and the atom names are also consistent). 
Here's a portion of the pdb file that I used:

ATOM   1759  N   LCK B  20      -3.985  -0.668   6.218  1.00
 20.00           N
ATOM   1760  CA  LCK B  20      -3.534  -1.515   5.127  1.00 20.00           C
ATOM   1761  C   LCK B  20      -2.096  -1.976   5.372  1.00 20.00           C
ATOM   1762  O   LCK B  20      -1.823  -3.174   5.413  1.00 20.00           O
ATOM   1763  HA  LCK B  20      -4.173  -2.398   5.113  1.00 20.00           H
ATOM   1764  CB  LCK B 
 20      -3.662  -0.780   3.790  1.00 20.00           C
ATOM   1765 1HB  LCK B  20      -4.701  -0.500   3.623  1.00 20.00           H
ATOM   1766 2HB  LCK B  20      -3.084   0.143   3.823  1.00 20.00           H
ATOM   1767  CG  LCK B  20      -3.171  -1.655   2.635  1.00 20.00           C
ATOM   1768 1HG  LCK B  20      -2.125  -1.918   2.792  1.00 20.00           H
ATOM  
 1769 2HG  LCK B  20      -3.735  -2.588   2.616  1.00 20.00           H
ATOM   1770  CD  LCK B  20      -3.326  -0.932   1.296  1.00 20.00           C
ATOM   1771 1HD  LCK B  20      -3.061   0.119   1.413  1.00 20.00           H
ATOM   1772 2HD  LCK B  20      -2.635  -1.356   0.567  1.00 20.00           H
ATOM   1773  CE  LCK B  20      -4.760  -1.047   0.774  1.00
 20.00           C
ATOM   1774 1HE  LCK B  20      -4.973  -2.081   0.503  1.00 20.00           H
ATOM   1775 2HE  LCK B  20      -5.463  -0.771   1.560  1.00 20.00           H
ATOM   1776  NZ  LCK B  20      -4.955  -0.170  -0.403  1.00 20.00           N
ATOM   1777  HZ  LCK B  20      -5.909  -0.258  -0.736  1.00 20.00           H
ATOM   1778  HN  LCK B  20      -3.255 
 -0.255   6.762  1.00 20.00           H

Any suggestion as to how to solve this error?  

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