Good afternoon,
I beg pardon, but I am a bit confused on how files are interacting. I previously used a “new” nucleic acid unit P. I created a parameter set for P in a file called P.frcmod. I made sure my pdb file (say DNA.pdb) had the new residue named “P”. I loaded some standard force field libraries by sourcing leaprcFF99SB. My flow in leap was something like
source leaprc.FF99SB
loadamberparams P.frcmod
foo=loadpdb DNA.pdb
1.) In your example, one loads a standard force field file, then a specialized library file (ABB.off), then the parameters for the special unit (ABD.frcmod).
In my former project, I had one parameter file for the “new” nucleic acid I used, a .frcmod file. Here, there seem to be two: the .frcmod and the .off. Are they serving distinct purposes, or was it just chosen to represent the parameters over two separate files?
2.) Is there a reason one is called ABD and the other is called ABB? I am concerned there is a meaning to the names which is important that escapes me.
3.) I assume, separate from this, I need to prepare a .prepin file to connect the new unit to the DNA backbone?
I do apologize if my questions are rudimentary.
> On Apr 4, 2020, at 12:42 PM, Christina Bergonzo <cbergonzo.gmail.com> wrote:
>
> Hello,
>
> The ABB.off file is loaded as a library file using the "loadoff" command in
> leap.
> The off files contain the same information as .lib files (atom names,
> types, charges, coordinates of template).
> You need to load the off file, and the frcmod file as shown below.
>
> Additionally - you will need to modify your PDB file.
> I am sending you a test.pdb and a test.ABB.pdb with the abasic site
> incorporated into it, so you can see how the residue is denoted.
> The files are old so they use outdated PDB naming conventions (for DNA this
> means switching OP1/OP2 to O1P/O2P, and changing the H5'/'' to H5'1/H5'2
> and H2'/'' to H2'1/H2'2, though I just delete hydrogens and let leap build
> them in). You should probably update the atom names if you want to use them
> without editing PDBs all the time...
>
> Leap commands I used here (loading the leaprc necessitates having
> $AMBERHOME set, and I specify a local path for the abasic site parameters
> location):
>
> source leaprc.DNA.OL15
> loadoff ~/bin/lib/ABB.off
> loadamberparams ~/bin/lib/ABD.frcmod
> mol = loadpdb test.pdb
> set default PBradii mbondi2
> saveamberparm mol test.ABB.parm7 test.ABB.rst7
> savepdb mol test.ABB.pdb
>
> Good luck!
> -Christina
>
> On Sat, Apr 4, 2020 at 11:56 AM Robert Molt <rwmolt07.gmail.com> wrote:
>
>> 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
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>>
>>>> _______________________________________________
>>>> 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
>>
>
>
> --
> -----------------------------------------------------------------
> Christina Bergonzo
> Research Chemist
> Biomolecular Measurement Division, MML, NIST
> -----------------------------------------------------------------
> <test.ABB.pdb><test.pdb>_______________________________________________
> 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
Received on Sun Apr 05 2020 - 10:30:03 PDT
