[gmx-users] add new residue and new atom
Malihe Hasanzadeh
ml.hasanzadeh at gmail.com
Fri Jan 29 18:49:08 CET 2016
Dear Justin,
I know these Force fields as much as I can use them. I use always
AMBER99sb-ILDN in my simulations actually like this time, but I'm sorry for
notify name of force field as incomplete. I copied parameters of Lys
residue from .rtp file in AMBER99sb-ILDN for my new residue (KCX) and only
data of carbamyl group added to it (below) as I said before.
CX OQ1
CX OQ2
CX HX
Malihe
On Fri, Jan 29, 2016 at 8:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/29/16 12:22 PM, Malihe Hasanzadeh wrote:
>
>> Dear Justin,
>> Is there any way to get parameters of KCX residue for amber99sb-ildn?
>>
>
> Well, how did you get the ones you have? And are you familiar with what
> the differences are between AMBER99sb and AMBER99sb-ILDN?
>
> -Justin
>
> 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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> 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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>>>
> --
> ==================================================
>
> 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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