Okay, no problems, thank you very much Carlos !
I just wondered why sometimes tleap generates such solvent artifacts and
could it be avoided using some options in the tleap script changing the box
parameters ) ?
Yours sincerely
Enrico
Il giorno ven 26 apr 2024 alle ore 13:26 Carlos Simmerling <
carlos.simmerling.stonybrook.edu> ha scritto:
> The water "corridors" should be resolved if you use a good relaxation
> protocol, see the ambermd.org tutorials page for an example.
>
> On Fri, Apr 26, 2024, 4:47 AM Enrico Martinez <jmsstarlight.gmail.com>
> wrote:
>
>> Right, thank you very much for these very useful suggestions !
>>
>> So, basically I tried to include these 2 terminal phosphates in the model
>> adding the following in tleap script
>>
>> but as I've mentioned before, it adds two protons to the same groups and
>> then tells that these protons are not found in parameters (so probably
>> there is also a trick with the protonation states of the phosphates).
>>
>> Otherwise If I just remove these
>>
>> ATOM 30460 P DG5 1922 120.480 71.998 142.128 1.00 0.00
>> P
>> ATOM 30461 OP1 DG5 1922 120.458 72.622 143.480 1.00 0.00
>> O
>> ATOM 30462 OP2 DG5 1922 121.228 70.728 141.928 1.00 0.00
>> O
>>
>> then everything works OK.
>>
>>
>> BTW what should I do with these strange "water corridors" generated by
>> tleap during the solvation, as shown on the screenshot in my previous
>> message ?
>>
>> Yours sincerely 🔆
>>
>> Enrico
>>
>> Il giorno ven 26 apr 2024 alle ore 02:13 Carlos Simmerling <
>> carlos.simmerling.stonybrook.edu> ha scritto:
>>
>>> I'll add to this some general advice for anyone that isn't aware of
>>> this- it is really worth reading the validation report for any pdb
>>> structure that you plan to use. It's full of good info and the link is
>>> right on the page for that pdb code. Among other things, it tells you about
>>> things present in the sample but not in the model, as well as regions that
>>> have poor fit to the density, and more.
>>>
>>> On Thu, Apr 25, 2024, 7:30 PM He, Amy via AMBER <amber.ambermd.org>
>>> wrote:
>>>
>>>> Hi Enrico!
>>>>
>>>> I took a closer look at the questioned PDB 5FKW. In this structure, the
>>>> 5’ end of the template has a phosphate groups because the true 5’ end is
>>>> missing. You can compare the present sequence with the reported sequence on
>>>> the paper. Additionally, you can find the information for missing residues
>>>> in the PDB file by the end of this section:
>>>>
>>>> REMARK 465 M RES C SSSEQI
>>>>
>>>> The following documentation might be helpful if you’re unfamiliar with
>>>> the format:
>>>>
>>>> https://www.wwpdb.org/documentation/file-format-content/format32/remarks2.html
>>>>
>>>> Hope this helps!
>>>>
>>>>
>>>> --
>>>> Amy He
>>>> Hadad Lab . OSU
>>>> He.1768.osu.edu
>>>>
>>>>
>>>> From: Enrico Martinez via AMBER <amber.ambermd.org>
>>>> Date: Thursday, April 25, 2024 at 3:08 AM
>>>> To: David A Case <dacase1.gmail.com>
>>>> Cc: AMBER Mailing List <amber.ambermd.org>
>>>> Subject: Re: [AMBER] Adding missing atoms of the DNA structure
>>>> Ah, yes sorry I forgot to add the PDB code, this is it:
>>>>
>>>> https://urldefense.com/v3/__https://www.rcsb.org/structure/5FKW__;!!KGKeukY!xwa2BEW2zLD_LpOjZTjRVs1sSv5sRmKKkbCFu6R0H6qnxioC8xK0rz_93RJp8NeBL1PppFA7OWLsc_ibbfH3S17gWEo$
>>>> <
>>>> https://urldefense.com/v3/__https:/www.rcsb.org/structure/5FKW__;!!KGKeukY!xwa2BEW2zLD_LpOjZTjRVs1sSv5sRmKKkbCFu6R0H6qnxioC8xK0rz_93RJp8NeBL1PppFA7OWLsc_ibbfH3S17gWEo$
>>>> >
>>>>
>>>> In the meantime I've just made parametrization of another structure
>>>> with a
>>>> much bigger fragment of DNA and it seems that it works fine without any
>>>> warnings from the Tleap.
>>>>
>>>> Enrico
>>>>
>>>> Il giorno mer 24 apr 2024 alle ore 18:21 David A Case <
>>>> dacase1.gmail.com>
>>>> ha scritto:
>>>>
>>>> > On Wed, Apr 24, 2024, Enrico Martinez wrote:
>>>> >
>>>> > >BTW why does this pdb has the phosphate group in the first residue
>>>> of DNA?
>>>> >
>>>> > I have no idea...I don't know where the file came from, and whether
>>>> the DNA
>>>> > was made synthetically or enzymatically.
>>>> >
>>>> > ...dac
>>>> >
>>>> >
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>>>>
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>>>> <
>>>> https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!xwa2BEW2zLD_LpOjZTjRVs1sSv5sRmKKkbCFu6R0H6qnxioC8xK0rz_93RJp8NeBL1PppFA7OWLsc_ibbfH3XE7cxzw$
>>>> >
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Received on Fri Apr 26 2024 - 06:30:02 PDT
