[gmx-users] add new residue and new atom
Malihe Hasanzadeh
ml.hasanzadeh at gmail.com
Fri Jan 29 18:13:46 CET 2016
Dear justin,
I forgot to write this step here, but I did this step also. I added (KCX
Protein) in .dat file. But unfortunately as you say the gromacs dosen't
identify my new residue!
What should I do? Is my added parameters for KCX residue correct?
Thanks
Malihe
On Fri, Jan 29, 2016 at 8:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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