Good morning fellow Covid-Zombies!
Drs. Bergonzo and Simmerling: your perspicacity and patience are
appreciated! Thank you!
I still have some confusions, if I may. I have previously worked with
using modified amino acid residues in a manner very similar to the
tutorial given by
https://ambermd.org/tutorials/basic/tutorial5/index.htm
I am extremely appreciative of your frcmod file; you are kind to help a
fellow scientist with no benefit. I am confused on the .off file? What
is its purpose? I am used to prepin files to "inform" how a unit fits
inside a polymerization; is a .off file serving a similar purpose? I
cannot find the term in the manual?
On 3/30/20 2:21 PM, Christina Bergonzo wrote:
> Hello,
>
> Yes, Carlos is right.
> In your example, you would rename the "48Z" residue in your PDB file as
> "ABB" and then the loaded off and prep files would be used.
> Alternatively, you can rename the library files to match the residue you
> have.
> But by necessity, you'll need to call this something other than DA or DC,
> since leap would just build in those entire nucleobases based on those
> residue names.
>
> -Christina
>
> On Mon, Mar 30, 2020 at 1:14 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> I think Christina was suggesting that you use a new residue name and
>> library, then the base won't get added.
>> Look at this paper for an example
>> Active destabilization of base pairs by a DNA glycosylase wedge initiates
>> damage recognition
>> Kuznetsov, N. A., Bergonzo, C., Campbell, A. J., Li, H., Mechetin, G. V.,
>> de los Santos, C., Grollman, A. P., Fedorova, O. S., Zharkov, D. O.,
>> Simmerling, C., Nucleic Acids Research, 2015, 43 (1), 272-281
>> DOI: 10.1093/nar/gku1300
>>
>> On Mon, Mar 30, 2020 at 1:08 PM Robert Molt <rwmolt07.gmail.com> wrote:
>>
>>> Good afternoon,
>>>
>>> I am very appreciative for the parameter suggestion, but unless I am
>>> confused, I do not see that it addresses the question I asked? I am
>>> confused about how to "leave a space" properly, and use the existing
>>> parameters?
>>>
>>> On 3/30/20 11:07 AM, Christina Bergonzo wrote:
>>>> Hello,
>>>>
>>>> In the past (the way past - 2011!) we have used these parameters:
>>>> https://www.ncbi.nlm.nih.gov/pubmed/17323932
>>>>
>>>> Kun Song created these leap files while in Carlos Simmerling's lab.
>>>> I attached the off and frcmod files to this email, as well as a
>> picture.
>>>> Please make sure they are compatible with any changes to the DNA FF
>> since
>>>> 2007!
>>>>
>>>> -Christina
>>>>
>>>> On Mon, Mar 30, 2020 at 10:36 AM Robert Molt <rwmolt07.gmail.com>
>> wrote:
>>>>> Good morning,
>>>>>
>>>>> I am attempting to simulate abasic DNA with a protein "bonded" to said
>>>>> DNA structure. In particular, an amino acid ends up "occupying" the
>>>>> "empty" location of the abasic DNA.
>>>>>
>>>>> In attempting to figure out the best way to construct this in Amber, I
>>>>> found the following post:
>>>>>
>>>>> http://archive.ambermd.org/201901/0211.html
>>>>>
>>>>> in which Dr. Case elaborates that one might "remove the base from A,
>>>>> replacing it with a hydrogen."
>>>>>
>>>>> I think I have a misunderstanding of how leap works for which I seek
>>>>> clarification.
>>>>>
>>>>> I have a "residue" named 48Z which is the phosphate backbone in my
>>>>> crystal structure associated with the abasic site. I think I have to
>>>>> "name" this residue something akin to "DA" or "DC" in order to tell
>> leap
>>>>> to connect the phosphate backbone properly (it expects to connect the
>>>>> polymer). But to my understanding, the act of doing so will
>>>>> automatically tell leap to fill in the missing heavy atoms? This seems
>>>>> to be the behavior when I attempt this.
>>>>>
>>>>> --
>>>>> Dr. Robert Molt Jr.
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>> _______________________________________________
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>>> --
>>> Dr. Robert Molt Jr.
>>>
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>>>
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>>
>
--
Dr. Robert Molt Jr.
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Received on Sat Apr 04 2020 - 09:00:01 PDT
