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
>>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Robert Molt Jr.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 30 2020 - 10:30:02 PDT
