Hi friends,
On a related issue: 
I'd like to explore the effect of replacing Val by Asp on the electrostatic  potential  'seen' by a cofactor which is completely surrounded by the protein  (this is relevant for understanding the change in reaction rate following such replacement). I thought of the following steps:

  1. Omit the cofactor from the pdb2pqr and APBS.
  2. Read into chimerax the complete pdb (i.e. including the cofactor).
  3. Generate the surfaces (protein and cofactor).
  4.  Render the electrostatic potential on both surfaces (i.e. Cofactor and protein surrounding it) and probe the potential on the cofactor.
  5. Does it make sense? Does APBS generate potential values in the void where the cofactor resides even though it wasn't present in the input pdb2pqr (i.e. in the void where the cofactor resides).
I'd appreciate your input.
Boaz

 
 
Boaz Shaanan, Ph.D.                                        
Dept. of Life Sciences                                     
Ben-Gurion University of the Negev                         
Beer-Sheva 84105                                           
Israel                                                     
                                                           
E-mail: bshaanan@bgu.ac.il
    
 
 
                

From: chimerax-users-request@cgl.ucsf.edu <chimerax-users-request@cgl.ucsf.edu>
Sent: Friday, 14 March 2025 21:00
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Subject: ChimeraX-users Digest, Vol 99, Issue 28
 
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Today's Topics:

   1. sybyl vs amber atom types in ChimeraX (laurene.jacquot)
   2. Re: sybyl vs amber atom types in ChimeraX (David A Case)


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Message: 1
Date: Fri, 14 Mar 2025 09:47:39 +0000
From: "laurene.jacquot" <laurene.jacquot@etu.chimieparistech.psl.eu>
Subject: [chimerax-users] sybyl vs amber atom types in ChimeraX
To: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu>
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Dear ChimeraX community,

I hope this message finds you well.

I am a master student currently working on a project where I need to generate a mol2 file with amber atom types for a protein.
Chimera does not manage to parametrize my protein at all, which is why I switched to ChimeraX.
ChimeraX does manage to generate a mol2 file, but it writes sybyl atom types. Despite looking on forums, I have not found a feature like in Chimera to write amber atom types instead.

I was wondering if such a feature exists in ChimeraX ?

Thanks in advance,
Best,
Laurène Jacquot
PSL University, ChimieParisTech

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Message: 2
Date: Fri, 14 Mar 2025 09:08:36 -0600
From: David A Case <dacase1@gmail.com>
Subject: [chimerax-users] Re: sybyl vs amber atom types in ChimeraX
To: "laurene.jacquot" <laurene.jacquot@etu.chimieparistech.psl.eu>,
        chimerax-users@cgl.ucsf.edu
Message-ID: <20250314150836.x2iskz4ufcygpsqt@pop-os.localdomain>
Content-Type: text/plain; charset=us-ascii; format=flowed

On Fri, Mar 14, 2025, laurene.jacquot via ChimeraX-users wrote:
>
>I am a master student currently working on a project where I need to
>generate a mol2 file with amber atom types for a protein.

I don't have a ChimeraX answer here, but rather a question: why do you need
a protein mol2 file with Amber atom types?  Amber workflows would not create
a mol2 file for an entire protein; but of course, you may need such a file
for some other purpose.  If so, we may be able to find some Amber tools that
does this (or avoids needing it), if the ChimeraX folks themselves don't
have a solution.

....dave case


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