[gmx-users] add new residue and new atom

[Malihe Hasanzadeh]

Hi

I used a PDB structure for MD simulation which it has a carbamylated Lys
(KCX 220). This residue via carbamyl group bonded to metal in active site.
So I had to define new residue(KCX), I copied parameters of Lys residue and
added carbamyl group and added to .rtp file in amber force field
(99sb)(gromacs5.0.4). I bring KCX parameters in below:
   [ KCX ]
 [ atoms ]
     N    N           -0.34790     1
     H    H            0.27470     2
    CA    CT          -0.24000     3
    HA    H1           0.14260     4
    CB    CT          -0.00940     5
   HB1    HC           0.03620     6
   HB2    HC           0.03620     7
    CG    CT           0.01870     8
   HG1    HC           0.01030     9
   HG2    HC           0.01030    10
    CD    CT          -0.04790    11
   HD1    HC           0.06210    12
   HD2    HC           0.06210    13
    CE    CT          -0.01430    14
   HE1    HP           0.11350    15
   HE2    HP           0.11350    16
    NZ    N3          -0.38540    17
   HZ1    H            0.34000    18
   HZ2    H            0.34000    19
   HZ3    H            0.34000    20
     C    C            0.73410    21
     O    O           -0.58940    22
    CX    C            0.73410    23
    HX    H            0.27470    24
   OQ1    O           -0.58940    25
   OQ2    O           -0.58940    26
 [ bonds ]
     N     H
     N    CA
    CA    HA
    CA    CB
    CA     C
    CB   HB1
    CB   HB2
    CB    CG
    CG   HG1
    CG   HG2
    CG    CD
    CD   HD1
    CD   HD2
    CD    CE
    CE   HE1
    CE   HE2
    CE    NZ
    NZ   HZ1
    NZ   HZ2
    NZ   HZ3
    NZ    CX
     C     O
    -C     N
    CX   OQ1
    CX   OQ2
    CX    HX
 [ impropers ]
    -C    CA     N     H
    CA    +N     C     O
    NZ   OQ1    CX   OQ2

In addition this protein has two Ni ion, that I added its parameters in
.atp .itp and .dat files.
Also my ligand has a F ion that when I docked with the protein, it closed
to Ni ion in active site (distance 2.9 A). when I start MD simulation I
faced with two problems:

1. when I run pdb2gmx gives many warning:

Identified residue MET1 as a starting terminus.
Warning: Residue KCX220 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue ILE221 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue HIS222 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue GLU223 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue ASP224 in chain has different type (Protein) from starting
residue MET1 (Protein).
More than 5 unidentified residues at end of chain - disabling further
warnings.
Identified residue LEU219 as a ending terminus.

My protein has 570 residue, but as you see the gromacs identified residue
LEU219 as a ending terminus.!

2. when I used -missing option and continued my simulations, after energy
minimization, I extract em.pdb file and I saw the distance between NI ion
in active site with F ion in ligand is much more ( ~5 A) than before in
complex.pdb. This means my ligand isn't stable in active site and it is
moving away!

please help me. what is my mistake?why ligand moving away and why gromacs
doesn't identify end of the protein? Is there a relationship between added
parameters and getting away of ligand?

Thanks