Indeed, that tutorial is a great resource for the general process of
building a modified amino acid. But, yes, it would be nice to have a
centralized database to keep track of parameters that people have already
developed. Not sure anyone wants the job of maintaining that database :)
To help people searching in the future, the set of parameters loaded by
that leaprc.xFPchromophores file are: eGFP, eBFP, eYFP, eCFP,DsRed, and
mCherry.
Cheers,
Brent
On Sun, Jul 7, 2024 at 11:42 PM He, Amy <he.1768.buckeyemail.osu.edu> wrote:
> I totally agree with that, we should check if there are existing parameter
> files (would be great to make a searchable database of the exisiting lib
> files). My reply was to the discussion on the GFP tutorial (
> https://ambermd.org/tutorials/basic/tutorial5/index.php), which was
> intended to explain the process of developing such parameters.
>
>
>
> *From: *Brent Krueger <kruegerb.hope.edu>
> *Date: *Sunday, July 7, 2024 at 8:06 PM
> *To: *He, Amy <he.1768.buckeyemail.osu.edu>, AMBER Mailing List <
> amber.ambermd.org>
> *Cc: *Ingso Limbu <i.limbu.student.uq.edu.au>
> *Subject: *Re: [AMBER] Modified amino acids: Simulating the Green
> Fluorescent Protein and Building a Modified Amino Acid Residue
>
> I'm not sure what you are staring from in terms of structure, but if your
> starting structure has GFP in it already, then this can be fairly simple.
> Section 3. 10. 1 of the Amber24 manual mentions built in libraries that
> are available for
>
> I'm not sure what you are staring from in terms of structure, but if your
> starting structure has GFP in it already, then this can be fairly simple.
> Section 3.10.1 of the Amber24 manual mentions built in libraries that are
> available for a handful of common fluorescent protein chromophores. If CRO
> is already in your PDB, then all you need to do is
> source leaprc.xFPchromophores (in addition to whatever parameters you are
> using for the rest of the system) before loading the PDB.
>
>
>
> Cheers,
>
> Brent
>
>
>
>
>
>
>
> On Wed, Jul 3, 2024 at 1:18 PM He, Amy via AMBER <amber.ambermd.org>
> wrote:
>
> Hi Ingso!
>
> I have had the same question before. (I could be wrong but) I think the
> hydrogens are removed here because their geometries don’t reflect the
> desired hybridization state of nitrogen. As long as the amide nitrogen is
> typed correctly after CRO gets embedded into the protein, the hydrogens can
> be fixed by leap.
>
> I prepare my input structures in the dipeptide form (unlike in this
> tutorial, which uses a CIF file of CRO in the free amino acid form), and as
> you said, usually, it’s not necessary to remove hydrogens. What to omit
> depends on the input structure, and how much of the input structure you
> want to embed into the protein. The
>
> I’m not following the discussion on MCPB, but to get more visibility I
> encourage you to write in a separate message to open a new thread for it :>
>
> Bests regards,
> Amy
>
>
> --
> Amy He
> Forli Lab . TSRI
> yihe.scripps.edu
>
>
> From: Ingso Limbu via AMBER <amber.ambermd.org>
> Date: Wednesday, July 3, 2024 at 9:57 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] Modified amino acids: Simulating the Green Fluorescent
> Protein and Building a Modified Amino Acid Residue
> Hi Amber community,
> Just wanted to point something out, as i was running on my system, in
> hopes of helping the community. For this tutorial, in the step of preparing
> of the mainchain file
> HEAD_NAME N1
> TAIL_NAME C3
> MAIN_CHAIN CA1
> MAIN_CHAIN C1
> MAIN_CHAIN N3
> MAIN_CHAIN CA3
> OMIT_NAME H2
> OMIT_NAME HN11 (Should only choose 1?)
> OMIT_NAME OXT
> OMIT_NAME HXT
> PRE_HEAD_TYPE C
> POST_TAIL_TYPE N
> CHARGE 0.0
>
> Why would we want to omit both Nitrogens hydrogen when we should only
> remove 1 H to mimic a peptide bond (unless i lack some knowledge on
> modified amino acids).
>
> Also while im asking questions on this email, i was curious on how exactly
> MCPB handles 2 metal centers? I havent tested it yet but was hoping to gain
> insight before i run it myself
>
> Thanks in advance 🙂
>
> Kind regards,
> Ingso
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> --
>
> ______________________________________________________
> Brent P. Krueger (he/him) (What's this?
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> ).......phone: 616 395 7629
> Professor.........................................................fax:
> 616 395 7118
> Hope College..................................................Schaap Hall
> 2120
> Department of Chemistry
> Holland, MI 49423
>
> Black Lives Matter | You are Welcome Here
>
--
______________________________________________________
Brent P. Krueger (he/him) (What's this?
<https://www.glsen.org/sites/default/files/GLSEN%20Pronouns%20Resource.pdf>).......phone:
616 395 7629
Professor.........................................................fax:
616 395 7118
Hope College..................................................Schaap Hall
2120
Department of Chemistry
Holland, MI 49423
Black Lives Matter | You are Welcome Here
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Received on Mon Jul 08 2024 - 09:00:02 PDT
