Document:

Form of Amendment and Joinder to Gas Gathering  Agreement

 Exhibit 10.4(d) 
 AMENDMENT AND JOINDER TO GAS GATHERING AGREEMENTS 
 THIS AMENDMENT AND JOINDER TO GAS GATHERING
AGREEMENTS (this “Amendment”) is made as of             , 2006, among Atlas Pipeline Partners, L.P., a Delaware limited partnership, and Atlas Pipeline Operating
Partnership, L.P., a Delaware limited partnership (collectively, “Gatherer”), Atlas America, Inc., a Delaware corporation (“Atlas America”), Resource Energy, LLC, a Delaware limited liability company
(formerly Resource Energy, Inc., “Resource Energy”), Viking Resources, LLC, a Pennsylvania limited liability company (formerly Viking Resources Corporation, “Viking Resources”), Atlas Noble, LLC, a
Delaware limited liability company (formerly Atlas Noble Corporation, “Atlas Noble”), Atlas Resources, LLC, a Pennsylvania limited liability company (formerly Atlas Resources, Inc., “Atlas Resources”),
Atlas Energy Resources, LLC, a Delaware limited liability company (“Atlas Energy”), and Atlas Energy Operating Company, LLC, a Delaware limited liability company (“Energy Operating”). 
 RECITALS 
 A. Gatherer and Atlas
America, Resource Energy and Viking Resources are parties to the Master Natural Gas Gathering Agreement dated February 2, 2000 (as amended as of October 25, 2005, the “2000 Gathering Agreement”) and desire to amend
the same in accordance with the terms hereof. 
 B. Gatherer and Atlas America (as successor to Atlas Energy Group, Inc.), Atlas Resources,
Atlas Noble, Resource Energy and Viking Resources are parties to the Natural Gas Gathering Agreement dated January 1, 2002 (as amended as of October 25, 2005, the “2002 Agreement” and with the 2000 Gathering
Agreement, the “Gathering Agreements”) and desire to amend the same in accordance with the terms hereof. 
 C. Atlas
America has formed Atlas Energy and Energy Operating for the purpose of facilitating the initial public offering of Atlas Energy and, pursuant to the Contribution and Assumption Agreement of even date herewith, is transferring all of the issued and
outstanding member interests in Resource Energy, Viking Resources, Atlas Noble and Atlas Resources to Energy Operating, and the parties hereto wish to join Atlas Energy and Energy Operating to the Gathering Agreements. 
 NOW, THEREFORE, in consideration of the premises, and the mutual covenants and agreements herein set forth, and intending to be legally bound, the
parties agree as follows: 
 1. Joinder in the Gathering Agreements. Effective as of the date hereof, each of Atlas Energy and Energy
Operating hereby joins each of the Gathering Agreements and accepts and agrees to be bound as a “Shipper” thereunder with respect to all of the terms and conditions thereof, and Gatherer hereby consents to such joinder and agrees that
Atlas Energy and Energy Operating are parties to the Gathering Agreements as the Shipper thereunder. 

 2. Removal of Atlas America from the 2002 Agreement. Effective as of the date hereof, Atlas
America is hereby removed as a party to the 2002 Gathering Agreement and shall have no further rights or obligations thereunder. 
 3.
Definition of “Investment Program.” The definition of “Investment Program” set forth in the 2000 Gathering Agreement is hereby amended and restated in its entirety as follows: 
 “Investment Program” means a Person principally engaged in the drilling of natural gas and oil wells for which Shipper or direct
or indirect subsidiary of Shipper acts as a general partner, managing partner or manager and the securities of which have been offered and sold to investors. 
 4. Other Terms of Gathering Agreements. Except as otherwise expressly provided herein, the Gathering Agreements are not amended, modified or affected by this Amendment. 
 5. Counterparts. This Amendment may be executed in any number of counterparts and by different parties hereto in separate counterparts, each of
which when so executed and delivered shall be deemed to be an original and all of which taken together shall constitute but one and the same instrument. Delivery of an executed counterpart of this Amendment by facsimile shall be equally as effective
as delivery of a manually executed counterpart of this Amendment. 
 [Signatures appear on following pages] 
  

 IN WITNESS WHEREOF, the parties have executed this Amendment to be effective as of the date first
written above. 
  

			
	Shipper:
	
	ATLAS AMERICA, INC.
		
	By:	 	  
	 Name:
	 	
	 Its:
	 	
	
	 ATLAS ENERGY RESOURCES, LLC

		
	By:	 	  
	 Name:
	 	
	 Its:
	 	
	
	 ATLAS ENERGY OPERATING COMPANY, LLC

		
	By:	 	 Atlas Energy Resources, LLC, its sole member

		
	By:	 	  
	 Name:
	 	
	 Its:
	 	
	
	RESOURCE ENERGY, LLC
		
	By:	 	 Atlas Energy Operating Company, LLC, its sole member

		
	By:	 	 Atlas Energy Resources, LLC, its sole member

		
	By:	 	  
	 Name:
	 	
	 Its:
	 	
	
	VIKING RESOURCES, LLC
		
	By:	 	 Atlas Energy Operating Company, LLC, its sole member

		
	By:	 	 Atlas Energy Resources, LLC, its sole member

		
	By:	 	  
	 Name:
	 	

			
	 Its:

	
	ATLAS NOBLE, LLC
		
	By:	 	 Atlas Energy Operating Company, LLC, its sole member

		
	By:	 	 Atlas Energy Resources, LLC, its sole member

		
	By:	 	  
	 Name:
	 	
	 Its:
	 	
	
	ATLAS RESOURCES, LLC
		
	By:	 	 AIC, LLC, its sole member

		
	By:	 	 Atlas Energy Operating Company, LLC, its sole member

		
	By:	 	 Atlas Energy Resources, LLC, its sole member

		
	By:	 	  
	 Name:
	 	
	 Its:
	 	
	
	Gatherer:
	
	 ATLAS PIPELINE OPERATING
 PARTNERSHIP,
L.P.

		
	By:	 	 Atlas Pipeline Partners GP, LLC, its general partner

		
	By:	 	  
	 Name:
	 	
	 Its:
	 	
	
	 ATLAS PIPELINE PARTNERS, L.P.

		
	By:	 	 Atlas Pipeline Partners GP, LLC, its general partner

		
	By:	 	  
	 Name:
	 	
	 Its:Form of Amendment and Joinder to Omnibus Agreement

 Exhibit 10.5(b) 
 AMENDMENT AND JOINDER TO OMNIBUS AGREEMENT 
 THIS AMENDMENT AND JOINDER TO OMNIBUS AGREEMENT
(this “Amendment”) is made as of             , 2006, among Atlas Pipeline Partners, L.P., a Delaware limited partnership, and Atlas Pipeline Operating
Partnership, L.P., a Delaware limited partnership (collectively, the “MLP”), Atlas America, Inc., a Delaware corporation (“Atlas America”), Resource Energy, LLC, a Delaware limited liability company
(formerly Resource Energy, Inc., “Resource Energy”), Viking Resources, LLC, a Pennsylvania limited liability company (formerly Viking Resources Corporation, “Viking Resources”), Atlas Energy Resources,
LLC, a Delaware limited liability company (“Atlas Energy”), and Atlas Energy Operating Company, LLC, a Delaware limited liability company (“Energy Operating”). 
 RECITALS 
 A.    The MLP, Atlas America, Resource Energy and Viking Resources are parties to the Omnibus Agreement dated February 2, 2000 (the “Omnibus Agreement”) and desire to amend the same in
accordance with the terms hereof. 
 B.    Atlas America has formed Atlas Energy and Energy Operating for the purpose of
facilitating the initial public offering of Atlas Energy and, pursuant to the Contribution and Assumption Agreement of even date herewith, is transferring all of the issued and outstanding member interests in Resource Energy and Viking Resources to
Energy Operating, and the parties hereto wish to join Atlas Energy and Energy Operating to the Omnibus Agreement. 
 NOW, THEREFORE,
in consideration of the premises, and the mutual covenants and agreements herein set forth, and intending to be legally bound, the parties agree as follows: 
 1.    Joinder in the Omnibus Agreement. Effective as of the date hereof, each of Atlas Energy and Energy Operating hereby joins the Omnibus Agreement and accepts and agrees to be bound as a
“Resource Entity” thereunder with respect to all of the terms and conditions thereof, except Section 5.2 thereof, and the MLP hereby consents to such joinder. 
 2.    Removal of Atlas America as Primary Obligor; Guaranty. Except to the extent that Atlas America purchases an asset that
is first properly presented to Atlas Energy as a Business Opportunity (as defined and as permitted by the Omnibus Agreement of even date herewith, between Atlas America and Atlas Energy, as the same may be amended from time to time), effective as of
the date hereof, Atlas America is hereby removed as a primary obligor of the Omnibus Agreement, and the MLP hereby consents to such removal. Atlas America hereby unconditionally and absolutely guarantees the performance of the Resource
Entities’ obligations arising under the Omnibus Agreement (the “Guaranteed Obligations”). If the Resource Entities fail or refuse to perform any Guaranteed Obligations, the MLP may make a demand upon Atlas 

 
America (a “Demand”). A Demand shall be in writing and shall reasonably and briefly specify in what manner any of the Resource
Entities has failed to perform under a Guaranteed Obligation, with a specific statement that the MLP is calling upon Atlas America to perform pursuant to this section. Atlas America agrees that except as expressly set forth herein, it will remain
bound under this section notwithstanding any defenses which, pursuant to the laws of suretyship, would otherwise relieve a guarantor of its obligations under a guarantee. Atlas America reserves the right to assert defenses which any of the Resource
Entities may have to performance of any Guaranteed Obligation other than defenses arising from the bankruptcy or insolvency of such Resource Entity and other defenses expressly waived hereby. 
 3.    Definitions. The following definitions set forth in the Omnibus Agreement are hereby amended and restated in their
entirety as follows: 
 “Investment Program” means a Person principally engaged in the drilling of natural gas and oil
wells for which a Resource Entity or a subsidiary of a Resource Entity acts as a general partner, managing partner or manager and the securities of which have been offered and sold to investors. 
 “Master Natural Gas Gathering Agreement” means the Master Natural Gas Gathering Agreement among the Resource Entities and the MLP
dated as of February 2, 2000, as amended from time to time. 
 4.    Consulting Services. Section 2.5 of
the Omnibus Agreement is hereby amended and restated as follows: 
 Consulting Services in Connection with Acquisitions. The Resource
Entities agree to assist the MLP in seeking to identify for possible acquisition Third Party Gathering Systems and to provide consulting services to MLP in evaluating and acquiring any such identified gathering system. Further, the Resource Entities
agree to give the MLP prompt written notice of the identification by any of them of any Third Party Gathering System for possible acquisition by such Resource Entity or any Affiliate (each, an “Identified Third Party Gathering
System”). Such notice shall set forth all information available to the Resource Entities about the Identified Third Party Gathering System, including the identity the gathering system and its seller and the proposed sales price, and
shall include all written information about the Identified Third Party Gathering System provided to the Resource Entities by or on behalf of the seller as well as any information or analyses compiled by the Resource Entities from other sources
(collectively, the “Business Opportunity Information”). The Resource Entities shall continue to provide promptly to the MLP any and all Business Opportunity Information subsequently received. Within a time period specified by
the Resource Entity’s notice to the MLP, which shall be a reasonable time under the circumstances, the MLP shall advise the Resource Entity in writing whether it wishes to 

  

 2 

 
acquire the Identified Third Party Gathering System. If the MLP advises the Resource Entity of its intent to acquire the Identified Third Party Gathering
System, the Resource Entities shall refrain from making an offer for the Identified Third Party Gathering System except as permitted hereunder. If the MLP (i) advises the Resource Entity that (with the approval of the conflicts committee of the
General Partner) it does not intend to acquire the Identified Third Party Gathering System, (ii) advises the Resource Entity of its intent to acquire the Identified Third Party Gathering System but does not complete the acquisition or
investment within a reasonable time after the MLP’s notice of its intent to the Resource Entity or (iii) fails to timely advise the Resource Entity of its intent, any of the Resource Entities shall be free to acquire the Identified Third
Party Gathering System. 
 5.    Construction Management Services. Article 3 of the Omnibus Agreement is hereby
amended and restated as follows: 
 In the event the MLP expands the Gathering System or constructs a new addition to the Gathering System,
whether pursuant to Article 2 or otherwise, the Resource Entities agree to cause a wholly-owned corporate subsidiary of Atlas Operating to provide to the MLP oversight of construction management in connection with any such expansion as requested by
the MLP. The MLP shall pay all third party construction costs related to any such expansion directly to the service provider for the construction Services related thereto. 
 6.    Other Terms of the Omnibus Agreement. Except as otherwise expressly provided herein, the Omnibus Agreement is not
amended, modified or affected by this Amendment. 
 7.    Counterparts. This Amendment may be executed in any
number of counterparts and by different parties hereto in separate counterparts, each of which when so executed and delivered shall be deemed to be an original and all of which taken together shall constitute but one and the same instrument.
Delivery of an executed counterpart of this Amendment by facsimile shall be equally as effective as delivery of a manually executed counterpart of this Amendment. 
  

 3 

 IN WITNESS WHEREOF, the parties have executed this Amendment to be effective as of the date first
written above. 
  

			
	Shipper:
	
	 ATLAS AMERICA, INC.

		
	By:	 	  
	 Name:
	 	
	 Its:
	 	
	
	 ATLAS ENERGY RESOURCES, LLC

		
	By:	 	  
	 Name:
	 	
	 Its:
	 	
	
	 ATLAS ENERGY OPERATING COMPANY, LLC

	 By:    Atlas Energy Resources, LLC, its sole member

		
	By:	 	  
	 Name:
	 	
	 Its:
	 	
	
	 RESOURCE ENERGY, LLC

	 By:    Atlas Energy Operating Company, LLC, its sole member

	
	 By:    Atlas Energy Resources, LLC, its sole member

		
	By:	 	  
	 Name:
	 	
	 Its:
	 	

  

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	 VIKING RESOURCES, LLC

	 By:    Atlas Energy Operating Company, LLC, its sole member

	
	 By:    Atlas Energy Resources, LLC, its sole member

		
	By:	 	  
	 Name:
	 	
	 Its:
	 	
	
	Gatherer:
	
	 ATLAS PIPELINE OPERATING PARTNERSHIP, L.P.

	
	 By:    Atlas Pipeline Partners GP, LLC, its general partner

		
	By:	 	  
	 Name:
	 	
	 Its:
	 	
	
	 ATLAS PIPELINE PARTNERS, L.P.

	
	 By:    Atlas Pipeline Partners GP, LLC, its general partner

		
	By:	 	  
	 Name:
	 	
	 Its:
	 	

  

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