[gmx-users] add new residue and new atom

[Justin Lemkul]

On 1/29/16 11:52 AM, Malihe Hasanzadeh wrote:
> 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?
>

You forgot step 5: 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

pdb2gmx writes your custom residue as its own chain, not bonded to the rest of 
the protein, so it is its own separate molecule.

-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

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