[gmx-users] add new residue and new atom
Malihe Hasanzadeh
ml.hasanzadeh at gmail.com
Fri Jan 29 18:22:57 CET 2016
Dear Justin,
Is there any way to get parameters of KCX residue for amber99sb-ildn?
Thanks
Malihe
On Fri, Jan 29, 2016 at 8:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/29/16 12:13 PM, Malihe Hasanzadeh wrote:
>
>> 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!
>>
>
> If this were true, pdb2gmx would not tell you otherwise. You didn't do
> what you thought you did, or you modified the wrong files.
>
> What should I do? Is my added parameters for KCX residue correct?
>>
>
> Follow the steps exactly in the link I provided. That's all there is to
> it.
>
> -Justin
>
> 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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>>> Gromacs Users mailing list
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>>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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