And you can find the corresponding solution in that paragraph as well.
> On Dec 7, 2020, at 3:29 PM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
> Hi Satyajit,
>
> If using GaussView works, you do not need to use VMD to try again.
>
> Based on your description, you might meet the problem mentioned in the second last paragraph of this tutorial: https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>.
>
> Pengfei
>
>> On Nov 21, 2020, at 5:01 AM, SATYAJIT KHATUA <satyajitkhatua09.gmail.com <mailto:satyajitkhatua09.gmail.com>> wrote:
>>
>> Hi,
>>
>> I have tried it with GaussView. First, I have created a valacy in the zinc
>> ion and then replaced it with a water molecule. After That, I have saved
>> the coordinates into a PDB file and followed subsequent steps as specified
>> in MCPB.py tutorial. After optimization and frequency calculation, I also
>> have a look into the fchk file to check whether there are any
>> discrepancies. But nothing suspicious is there. So I proceed further by
>> generating prmtop and inpcrd file for my MD run. I have minimized my system
>> with SHAKE by putting a weak restraint of 2.0. After minimization, I got
>> stuck into the heating process after step 37 with the error message:
>>
>> vlimit exceeded for step 37; vmax = 76.6693
>>
>> Coordinate resetting (SHAKE) cannot be accomplished,
>> deviation is too large
>> NITER, NIT, LL, I and J are : 0 3 4651 9219 9221
>>
>> Note: This is usually a symptom of some deeper
>> problem with the energetics of the system.
>>
>> nmropt was on during my heating process. I have checked the mdcrd file by
>> saving each step for nstlim=1000. Going with the atom ids, I found out that
>> something is going on between the O and a H atom of our newly created water
>> molecule. I don't know how to proceed further as I have tested and tried
>> almost every suggestion that was given in the amber archive. Is there
>> anything I have done wrong?
>>
>> I will definitely try to build the system with VMD again as per your
>> suggestion. Let's see what happens.
>>
>> Thanks,
>> Satyajit Khatua
>>
>>
>> ---------- Forwarded message ---------
>> Message: 13
>> Date: Fri, 20 Nov 2020 10:42:47 -0500
>> From: Pengfei Li <ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>>
>> Subject: Re: [AMBER] Tri-coordination environment in zinc
>> To: AMBER Mailing List <amber.ambermd.org <mailto:amber.ambermd.org>>
>> Message-ID: <E475C039-5450-4525-85C7-A3BED9A61E79.gmail.com <mailto:E475C039-5450-4525-85C7-A3BED9A61E79.gmail.com>>
>> Content-Type: text/plain; charset=us-ascii
>>
>> Hi Satyajit,
>>
>> Do you have graphic program like GaussView? GaussView can do such a job. I
>> guess VMD could also do that by using a plugin like Molefacture:
>> https://www.ks.uiuc.edu/Research/vmd/plugins/molefacture/ <https://www.ks.uiuc.edu/Research/vmd/plugins/molefacture/> <
>> https://www.ks.uiuc.edu/Research/vmd/plugins/molefacture/ <https://www.ks.uiuc.edu/Research/vmd/plugins/molefacture/>>.
>>
>> After you adding the coordinated water molecules and save the coordinates
>> into a PDB file, you can just copy the coordinates of the added water
>> molecules into your original PDB file with renaming that water residue
>> (renaming both residue name and atom names inside) consistent with the
>> AMBER naming scheme (residue name: HOH or WAT, and atom names are O, H1,
>> and H2), and resequencing the PDB file using pdb4amber.
>>
>> Hope it helps,
>> Pengfei
>>
>>> On Nov 3, 2020, at 12:06 AM, SATYAJIT KHATUA <satyajitkhatua09.gmail.com <mailto:satyajitkhatua09.gmail.com>>
>> wrote:
>>>
>>> Hi,
>>>
>>> Can you suggest to me any other tool to do so?
>>>
>>> with regards,
>>> Satyajit Khatua
>>>
>>>
>>> ---------- Forwarded message ---------
>>> Message: 6
>>> Date: Sun, 1 Nov 2020 10:35:31 -0800
>>> From: Bill Ross <ross.cgl.ucsf.edu <mailto:ross.cgl.ucsf.edu>>
>>> Subject: Re: [AMBER] Tri-coordination environment in zinc
>>> To: amber.ambermd.org <mailto:amber.ambermd.org>
>>> Message-ID: <eec483ff-eba4-ed99-e6d4-0dc151e5a5e3.cgl.ucsf.edu <mailto:eec483ff-eba4-ed99-e6d4-0dc151e5a5e3.cgl.ucsf.edu>>
>>> Content-Type: text/plain; charset=utf-8; format=flowed
>>>
>>> Yes. It's harder to do with xleap than other graphic editors, but still
>>> might only take a few minutes.
>>>
>>> Bill
>>>
>>> On 11/1/20 9:38 AM, SATYAJIT KHATUA wrote:
>>>> Hi,
>>>>
>>>> Thanks for replying. Here, I am talking about one water intending to
>>>> satisfy the metal site coordination. Can I place the water by hand using
>>>> the leap editor?
>>>>
>>>> with regards,
>>>> Satyajit Khatua
>>>>
>>>>
>>>> ---------- Forwarded message ---------
>>>> Message: 7
>>>> Date: Thu, 29 Oct 2020 23:59:57 -0700
>>>> From: Bill Ross <ross.cgl.ucsf.edu <mailto:ross.cgl.ucsf.edu>>
>>>> Subject: Re: [AMBER] Tri-coordination environment in zinc
>>>> To: amber.ambermd.org <mailto:amber.ambermd.org>
>>>> Message-ID: <9c0e181c-eae2-73db-90f6-a9f4970b1131.cgl.ucsf.edu <mailto:9c0e181c-eae2-73db-90f6-a9f4970b1131.cgl.ucsf.edu>>
>>>> Content-Type: text/plain; charset=utf-8; format=flowed
>>>>
>>>> If we're just talking about a few waters, why not just place them by
>> hand?
>>>>
>>>> Bill
>>>>
>>>>
>>>> On 10/29/20 10:39 PM, SATYAJIT KHATUA wrote:
>>>>> Hi,
>>>>>
>>>>> Sorry for replying this late. I thought that maybe using MCPB.py is a
>>>>> viable solution in this case and stopped following further updates
>> posted
>>>>> in the archive. Now, I understand the problems that I am going to face
>> if
>>>> I
>>>>> don't take care of this problem that you have mentioned. Previously, I
>>>> have
>>>>> also tried the modeling by striping the crystal waters of the PDB and
>>> then
>>>>> adding the suitable water box to see if any water molecule falls within
>>>> the
>>>>> coordination distance of zinc ion but none to avail. Can you please help
>>>> me
>>>>> with the ways about how to saturate the metal site with the water
>>>> molecule?
>>>>> That will be helpful.
>>>>>
>>>>> with regards,
>>>>> Satyajit Khatua
>>>>>
>>>>>
>>>>> ---------- Forwarded message ---------
>>>>> Message: 7
>>>>> Date: Thu, 22 Oct 2020 17:22:53 -0400
>>>>> From: Pengfei Li <ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>>
>>>>> Subject: Re: [AMBER] Tri-coordination environment in zinc
>>>>> To: AMBER Mailing List <amber.ambermd.org <mailto:amber.ambermd.org>>
>>>>> Message-ID: <2D91EE0A-7C34-4DFF-BA87-7654944421CE.gmail.com <mailto:2D91EE0A-7C34-4DFF-BA87-7654944421CE.gmail.com>>
>>>>> Content-Type: text/plain; charset=us-ascii
>>>>>
>>>>> Hi Satyajit,
>>>>>
>>>>> For this case maybe it is better for you to saturate the metal site
>> first
>>>>> with an additional water before the MCPB.py modeling. If the metal site
>>> is
>>>>> not saturated, it could be challenging to get meaningful results for the
>>>>> quantum calculations.
>>>>>
>>>>> Pengfei
>>>>>
>>>>>> On Sep 19, 2020, at 12:36 AM, SATYAJIT KHATUA <
>>> satyajitkhatua09.gmail.com <mailto:satyajitkhatua09.gmail.com>
>>>>> wrote:
>>>>>> Dear Users,
>>>>>>
>>>>>> Anyone here have worked with tri-coordination environment on zinc in
>>>>> protein?? Recently, I am working on a superantigen protein that contains
>>> a
>>>>> tri-coordinated environment (two bound His- and one Asp-) on zinc.
>>> Usually
>>>>> zinc possess a tetra-coordination. In crystallography paper, they told
>>>> that
>>>>> possibly there is a water molecule on fourth position although they
>> didnt
>>>>> find any signature on electron density map. So can someone give some
>>>> inputs
>>>>> about the parameterization of this zinc coordination through amber force
>>>>> fields?? Any suggestions about some tutorials or papers in this regard
>>>> will
>>>>> also be appreciated.
>>>>>> Thanks in advance,
>>>>>> Satyajit Khatua
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
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>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
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>>>>> AMBER mailing list
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>>>>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Dec 07 2020 - 13:00:04 PST
