Apologies for my brevity, I’m answering from my phone.
1. I don't know what you did in your other project, but it’s possibly different from what you need to do in this one. If you needed to modify already existing parameters, maybe a frcmod is all you needed then. Check the manual for an explanation of differences between the file types.
2. The ABB ABD designations are from the referenced paper.
3. No. Try the test example I sent, or make your own test to verify that those 2 files (and a DNA FF) are all you need to load.
-Christina
> On Apr 5, 2020, at 1:22 PM, Robert Molt <rwmolt07.gmail.com> wrote:
>
> 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 The files are old so they use outdated PDB naming conventions (for DNA this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
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>>>
>>
>>
>> --
>> -----------------------------------------------------------------
>> Christina Bergonzo
>> Research Chemist
>> Biomolecular Measurement Division, MML, NIST
>> -----------------------------------------------------------------
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Received on Sun Apr 05 2020 - 13:00:02 PDT
