<PAGE>
 
                                                                   EXHIBIT 10.39

                                 AMENDMENT OF 
                       AGREEMENT OF LIMITED PARTNERSHIP
                                      OF 
                   NATIONAL GOLF OPERATING PARTNERSHIP, L.P.


          THIS AMENDMENT OF AGREEMENT OF LIMITED PARTNERSHIP (this "Amendment"),
dated as of July 25, 1996, is entered into by National Golf Properties, Inc., a
Maryland corporation, as the general partner (the "General Partner") of National
Golf Operating Partnership, L.P., a Delaware limited partnership (the
"Partnership").

          WHEREAS, the General Partner and the limited partners of the
Partnership (the "Limited Partners") are parties to that certain Agreement of
Limited Partnership (the "Agreement"), dated a of August 18, 1993;

          WHEREAS, the General Partner has entered into an Asset Purchase
Agreement and Agreement and Plan of Merger (the "Acquisition Agreement"), dated
as of February 2, 1996 and amended on February 16, 1996, among the General
Partner, Golf Enterprises, Inc., a Kansas corporation, and GEI Acquisition 
Corporation, a Kansas corporation, pursuant to which Acquisition Agreement,
among other things, the General Partner has agreed to purchase the Purchased
Assets described therein, and has the right to assign such agreement in whole or
in part to the Partnership;

          WHEREAS, the General Partner intends to assign to the Partnership the
right to acquire an undivided partial interest in each of the Purchased Assets
and to pay cash therefor;

          WHEREAS, the General Partner intends to acquire the remaining interest
in the Purchased Assets and contribute them to the Partnership on the terms set
forth herein;

          WHEREAS, certain other changes to the definition of "Certificate of
Incorporation" and Sections 4.6 and 8.6.F of the Partnership Agreement are
necessary to reflect the General Partner's reincorporation as a Maryland
corporation and otherwise clarify and update such provisions; and

          WHEREAS, the General Partner has obtained the written consent to this
Amendment of Limited Partners representing at least the minimum number of
Partnership Interests (as defined in the Partnership Agreement) required to
amend the Partnership Agreement pursuant to Section 7.3 and Article 14 of the
Partnership Agreement, which written consent is attached as Exhibit A to this
Amendment.

          THEREFORE, pursuant to Section 7.3 and Article 14 of the Partnership
Agreement, the General Partner hereby amends the Partnership Agreement as
follows, effective as of the date of this Amendment.  Defined terms used in this
Amendment and not otherwise defined herein shall have the same meanings as such
terms have in the Partnership Agreement.

          The definition of "Certificate of Incorporation" in Article 1 is
hereby amended in its entirety as follows:

<PAGE>
 
          ""Certificate of Incorporation" means the Articles of Incorporation of
            ----------------------------
the General Partner file in the state of Maryland on August 31, 1995 as amended 
or restated from time to time."

          Section 4.5 of the Partnership Agreement is hereby amended by adding 
the following at the end of such section:

          "G.  Special Supplemental Capital Contribution by General Partner.
               ------------------------------------------------------------
Notwithstanding the other provisions contained in this Article 4, immediately
following the closing of the General Partner's acquisition of an interest in
certain golf course properties and related assets (the "Purchased Assets") from
Golf Enterprises, Inc., a Kansas corporation ("GEI"), pursuant to that certain
Asset Purchase Agreement and Agreement and Plan of Merger (the "Acquisition
Agreement"), dated as of February 2, 1996 and amended on February 16, 1996 by
that certain First Amendment to the Asset Purchase Agreement and Plan of Merger,
among the General Partner, GEI Acquisition Corporation, a Kansas corporation
("Newco") and GEI, the General Partner may contribute all of its interest in the
Purchased Assets collectively as a special supplemental Capital Contribution to
the Partnership. Upon such Capital Contribution, (i) the General Partner shall
be issued that number of Partnership Units equal to the number of shares of
Purchaser Common Stock (as defined in the Acquisition Agreement) issued as
Acquisition Consideration (as defined in the Acquisition Agreement) pursuant to
the Acquisition Agreement, (ii) the Agreed Value and the Gross Asset Value of
the Contributed Property shall be equal to $40,786,649 (except in the event that
the number of shares of Purchaser Common Stock to be issued as Acquisition
Consideration has been limited by the maximum or minimum share issuance
provisions of Section 1.5(a)(i) of the Acquisition Agreement, in which case the
Agreed Value and the Gross Asset Value of the Contributed Property shall be
equal to the number of shares of Purchaser Common Stock issued as Acquisition
Consideration times the Average Purchaser Common Stock Price (as defined in the
Acquisition Agreement)), (iii) Exhibit A to this Agreement shall be
appropriately amended to reflect such issuance and the corresponding adjustments
in the Percentage Interest of each of the Partners, as well as the Agreed Value
and the Gross Asset Value of the Contributed Property, and (iv) the Capital
Account of the General Partner shall be appropriately adjusted. Following the
General Partner's contribution of its interest in the Purchased Assets to the
Partnership, the General Partner shall promptly give each Partner written notice
of its Percentage Interest and their Percentage Interests as adjusted. This
Paragraph G of Section 4.5 shall not be construed to permit any Capital
Contribution other than the contribution of the General Partner's interest in
the Purchased Assets by the General Partner."

          Section 4.6 of the Partnership Agreement is hereby amended in its 
entirety as follows:

          "Section 4.6  Stock Option Plan
                        -----------------

          If at any time or from time to time the General Partner is required,
pursuant to the Stock Incentive Plan, to make a contribution of REIT Shares to
the Partnership, such contribution shall be treated as an additional Capital
Contribution as provided in Section 4.5, in an amount equal to the Value
(provided, that, for these purposes, only the trading day on which
 --------

                                       2


<PAGE>
 
the General Partner contributes such REIT Shares to the Partnership shall be 
considered) multiplied by the number of REIT Shares contributed by the General 
            ---------- --
Partner to the Partnership. In consideration for such contribution, the General
Partner's Capital Account shall be adjusted as provided in this Agreement and
the General Partner shall be issued a number of Partnership Units equal to the
number of REIT Shares so contributed. Furthermore, if at any time or from time
to time the General Partner issues or sells REIT Shares pursuant to the Stock
Incentive Plan (other than a contribution to the Partnership as provided above),
it may contribute the proceeds therefrom to the Partnership as an additional
Capital Contribution as provided in Section 4.5. In consideration for such
contribution, the General Partner's Capital Account shall be adjusted as
provided in this Agreement and the General Partner shall be issued a number of
Partnership Units equal to the number of REIT Shares so issued or sold.
Notwithstanding the foregoing, the preemptive rights provided in Section 4.5.E.
shall not apply to the Capital Contributions described above in this Section
4.6."

          Section 7.6.C of the Partnership Agreement is hereby amended by adding
the following at the end of such section:

          "The General Partner also is expressly authorized to cause the
Partnership to issue to it Partnership Units corresponding to REIT Shares issued
or sold by the General Partner pursuant to the Stock Option Plan or any similar
or successor plan and to repurchase such Partnership Units from the General
Partner to the extent necessary to permit the General Partner to repurchase such
REIT Shares in accordance with such plan."

          Section 8.6.F of the Partnership Agreement is hereby amended in its 
entirety as follows:

               "F. Notwithstanding the provisions of this Section 8.6 or any
other provision of this Agreement, a Limited Partner (i) shall not be entitled
to effect an Exchange to the extent the ownership or right to acquire REIT
Shares pursuant to such Exchange) by such Partner would cause such Partner or
any other Person to violate the restrictions on ownership and transfer of REIT
Shares set forth in the Certificate of Incorporation and (ii) shall have no
rights under this Agreement to acquire REIT Shares which would otherwise be
prohibited under the Certificate of Incorporation. To the extent any attempted
Exchange would be in violation of this Section 8.6.F., it shall be null and void
ab initio and such Limited Partner shall not acquire any rights or economic
interest in the REIT Shares otherwise issuable upon such Exchange."

          The definition of "Stock Option Plan" in the Partnership Agreement is 
hereby amended in its entirety as follows:

          ""Stock Option Plan" means the 1993 Stock Option and Incentive Plan 
            -----------------
for Key Employees of National Golf Properties, Inc., National Golf Operating
Partnership, L.P. and American Golf Corporation and The 1995 Independent
Director Equity Participation Plan of National Golf Properties, Inc. or any
similar or successor plans."

                                       3

<PAGE>
 
          Except as modified by the preceding paragraphs, the Partnership 
Agreement shall continue in effect in accordance with all of the terms and 
conditions contained therein.

          IN WITNESS WHEREOF, the General Partner has executed this Amendment as
of the date first written above.

                                                  NATIONAL GOLF PROPERTIES, INC.


                                                  By:  /s/ Richard C Price
                                                       -------------------
                                                       Richard C. Price
                                                       President

                                       4

<PAGE>
 
                                   EXHIBIT A
                                   ---------

                                WRITTEN CONSENT
                            OF THE LIMITED PARTNERS
                                      OF
                   NATIONAL GOLF OPERATING PARTNERSHIP, L.P.

          The undersigned, as the limited partners (the "Limited Partners") of
National Golf Operating Partnership, L.P., a Delaware limited partnership (the
"Partnership"), hereby consent to the proposed Amendment of Agreement of Limited
Partnership of National Golf Operating Partnership, L.P., dated as of July 25,
1996, to be entered into by National Golf Properties, Inc., a Maryland
corporation, as the general partner of the Partnership (the "General Partner").

          This Written Consent also shall constitute a Consent (pursuant to
Section 7.5 of the Partnership Agreement) by the Limited Partners to the General
Partner's purchase of certain properties owned by Golf Enterprises, Inc., a
Kansas corporation ("GEI"), pursuant to that certain Asset Purchase Agreement
and Agreement and Plan of Merger, dated as of February 2, 1996 and amended on
February 16, 1996, among the General Partner, GEI and GEI Acquisition
Corporation.

          This Written Consent may be executed in two or more counterparts, all
of which shall be considered one and the same agreement and it being understood
that all parties need not sign the same counterpart.


                                             __________________________________
                                             David G. Price


                                             The Joan P. Anawalt Revocable Trust
                                             dated July 29, 1985, as amended


                                             /s/ Joan P. Anawalt Ttee
                                             ----------------------------------
                                             By: 
                                             Its:

                                      A-1
<PAGE>
 
                                          The Joan P. Anawalt Income Trust
                                          dated August 23, 1988, as amended
                                                                                

                                          /s/ Joan P. Anawalt Ttee
                                          ------------------------
                                          By:
                                          Its:

                                          The Joan P. Anawalt 1993 Annuity Trust
                                          dated August 3, 1993, as amended
                                                                                

                                          /s/ Joan P. Anawalt Ttee   
                                          ------------------------
                                          By:
                                          Its:

                                          AMERICAN GOLF CORPORATION,
                                          a California corporation
                                                                                

                                          ________________________
                                          By:
                                          Its:

                                          SUPERMARINE AVIATION, LIMITED,
                                          a California corporation
                                                                                

                                          ________________________
                                          By:
                                          Its:

                                      A-2
<PAGE>
 
                                          RSJ GOLF, INC.,
                                          a California corporation
                                                                                

                                          _______________________
                                          By:
                                          Its:
                                             
                                          /s/ Richard C. Price
                                          ------------------------
                                          Richard C. Price         


                                          /s/ Sheri L. Price
                                          ------------------------
                                          Sheri L. Price         

                                          /s/ Edward R. Sause
                                          ------------------------
                                          Edward R. Sause

                                          /s/ Barbara M. Colton
                                          ------------------------
                                          Barbara M. Colton

                                          
                                          ________________________
                                          Richard Bermudez

                                          /s/ Ernst C. Burns
                                          ------------------------
                                          Ernst C. Burns

                                          /s/ Robert H. Williams
                                          ------------------------
                                          Robert H. Williams

                                      A-3
<PAGE>
 
                                   EXHIBIT A
                                   ---------

                                WRITTEN CONSENT
                            OF THE LIMITED PARTNERS
                                      OF
                   NATIONAL GOLF OPERATING PARTNERSHIP, L.P.

          The undersigned, as the limited partners (the "Limited Partners") of 
National Golf Operating Partnership, L.P., a Delaware limited partnership (the 
"Partnership"), hereby consent to the proposed Amendment of Agreement of Limited
Partnership of National Golf Operating Partnership, L.P., dated as of July 25,
1996, to be entered into by National Golf Properties, Inc., a Maryland
corporation, as the general partner of the Partnership (the "General Partner").

          This Written Consent also shall constitute a Consent (pursuant to 
Section 7.5 of the Partnership Agreement) by the Limited Partners to the General
Partner's purchase of certain properties owned by Golf Enterprises, Inc., a 
Kansas corporation ("GEI"), pursuant to that certain Asset Purchase Agreement 
and Agreement and Plan of Merger, dated as of February 2, 1996 and amended on 
February 16, 1996, among the General Partner, GEI and GEI Acquisition 
Corporation.

          This Written Consent may be executed in two or more counterparts, all 
of which shall be considered one and the same agreement and it being understood 
that all parties need not sign the same counterpart.


                                        /s/ David G. Price                    
                                        -----------------------               
                                        David G. Price                        
                                                                              
                                        The Joan P. Anawalt Revocable Trust   
                                        dated July 29, 1985, as amended       
                                                                              
                                                                              
                                        _______________________               
                                        By:                                   
                                        Its:                                   

                                      A-1
<PAGE>
 
                                          The Joan P. Anawalt Income Trust
                                          dated August 23, 1988, as amended
                                                                                


                                          _______________________
                                          By:
                                          Its:

                                          The Joan P. Anawalt 1993 Annuity Trust
                                          dated August 3, 1993
                                                                                


                                          _______________________
                                          By:
                                          Its:

                                          AMERICAN GOLF CORPORATION,
                                          a California corporation
                                                                                
                                          /s/ David G. Price
                                          -----------------------
                                          By:
                                          Its:

                                          SUPERMARINE AVIATION, LIMITED,
                                          a California corporation
                                                                                
                                          /s/ David G. Price
                                          -----------------------
                                          By:
                                          Its:

                                      A-2
<PAGE>
 
                                          RSJ GOLF, INC.,
                                          a California corporation
                                                                                
                                          /s/ David G. Price 
                                          -----------------------
                                          By:
                                          Its:
                                             
                                          /s/ Richard C. Price
                                          ------------------------
                                          Richard C. Price         


                                          ________________________
                                          Sheri L. Price         

                                          /s/ Edward R. Sause
                                          ------------------------
                                          Edward R. Sause


                                          ________________________
                                          Barbara M. Colton

                                          
                                          ________________________
                                          Richard Bermudez


                                          ________________________
                                          Ernst C. Burns


                                          ________________________
                                          Robert H. Williams

                                      A-3