[gmx-users] add new residue and new atom
Malihe Hasanzadeh
ml.hasanzadeh at gmail.com
Sat Jan 30 17:36:43 CET 2016
Dear Justin,
I did step by step to add new residue and new atom again and finally was
done. But still there is last problem, as I said before, my ligand has a F
ion that bonded to Ni ion in active site (distance 2.6 A), after N.V.T
ligand is moving away and distance between F and Ni is 5 A. What causes the
ligand away from the active site? How can keep the ligand in bonded to Ni
in active site? Is there problem from .mdp or ...?
Thanks
Malihe
On Fri, Jan 29, 2016 at 9:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/29/16 12:49 PM, Malihe Hasanzadeh wrote:
>
>> 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
>>
>
> You have a simple issue of an absent assignment of residue type in
> residuetypes.dat that triggers this problem. I don't know why we're
> re-hashing the details of an .rtp entry that has already been constructed.
> That's not your problem.
>
> -Justin
>
> 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
>>>>>>>
>>>>>>> * Please search the archive at
>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>> posting!
>>>>>>>
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>>>>>>>
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>>>>>>> or
>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>> ==================================================
>>>>>
>>>>> 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
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
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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
>>>
>>> * Please search the archive at
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>>> posting!
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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
>
> * Please search the archive at
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> posting!
>
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>
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