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Department of Bioorganic Chemistry

If you are interested in the PSEUROT program (the original versions or the one with our modifications), please contact Prof. Cornelis Altona in The Netherlands to clear license matters with him first.


What is PSEUROT+JHF ?

  • The original 'PSEUROT' (version 3B) program was modified by Janez Plavec, National Institute of Chemistry, Ljubljana, Slovenia, Anders Sandström and Christophe Thibaudeau, Department of Bioorganic Chemistry, BMC, Uppsala University between December 1997 - March 1998.

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  • The modified version, called 'PSEUROT+JHF', allows to perform the conformational analysis of the pentofuranose moiety in fluoronucleosides basing upon 3JHH and / or 3JHF vicinal coupling constants. For 3JHF coupling constants, we have parametrized a 7-parameter Karplus equation (including the effect of bond angle changes) using a dataset composed both of nucleosides and conformationally constrained fluorinated compounds (J. Org. Chem., 1998, 63, 4967-4984)

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    Changes made to the original PSEUROT (version 3B) program to obtain PSEUROT+JHF.

    The original 'PSEUROT' program was developed by Prof. C. Altona et al. at the University of Leiden in the Netherlands in the early 1980's and they have since then made several modifications and enhancements to this program. The following changes have been made to the source code of the original PSEUROT (v. 3B) program to obtain the PSEUROT+JHF modified version.

    It should be noted that all line numbers indicated in this page correspond to the real line numbers in the original PSEUROT.f (version 3B) file, NOT to the numbers indicated either on the left or right of some of the lines in that file!


    (I) Changes in the Input Description Section

    Changes related to CARDSET 3 (NAME,NEWP,FASE,A,B,(SUB(I),I=1,4) (A8,I2,7F10.0))

    The input file for the modified PSEUROT+JHF program allows to define:

    Therefore, the parameter NEWP in the PSEUROT+JHF program can be set to 3 values and the original lines 29 and 30 in the section describing the input format of PSEUROT (v. 3B) should be substituted for the followings in PSEUROT+JHF:
            C       NEWP   --> IF NEWP.EQ.1 A NEW SET OF KARPLUS     
            C                  PARAMETERS IS READ FROM A SECOND CARD for
            C                  H-H couplings (10F8.0)
            C              --> IF NEWP.EQ.2 A NEW SET OF SEVEN 
            C                  (A-G in J. Org. Chem.,1998, 63, 4967-4984)      
            C                  KARPLUS PARAMETERS IS READ FROM A SECOND CARD for
            C                  H-F couplings and two bond angles (10F8.0)
            C              --> IF NEWP.EQ.0 A SET OF KARPLUS PARAMETERS      
            C                  for H-H couplings is used (1980)
    In order to perform the conformational analysis of fluoronucleosides on the basis of 3JHH and 3JHF coupling constants, we have used lambda electronegativities, not the Huggins scale, as in the case of the original PSEUROT (v. 3B) program. This is now explicitely mentioned in the description of the input format:
            C               SUB(I),I=1,4 --> lambda ELECTRONEGATIVITY OF SUBSTITUENTS;       
            C               NOTE: THE POSITION OF SUB(I) DEFINES THE SIGN:
            C               SUB(1) AND SUB(3) ARE REGARDED 'POSITIVE' 
            C               SUB(2) AND SUB(4) ARE REGARDED 'NEGATIVE'

    (II) Changes in the section of declaration of variables (in particular, introduction of 'scalfact', the scale factor that is applied during the minimization procedure to the errors of 3JHF couplings compared to 3JHH couplings):

     

     
     
     
     
     
     
     

    The following lines have been added in the section from the original program between lines 67 and 90 :


    (III) Changes made to the rest of the program itself

  • R means that the given changes should replace the indicated lines in the original PSEUROT (version 3B) program
  • I means that the change has to be inserted before (ib)or after (ia) the indicated line.

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    Line 90 (R):

    Line 93 (R):

    Line 100 (R):

    Line 102 (IB):

    Line 110 (IB):

    Line 111 (R):

    Line 112 (R):

    Line 120 (IB):

    Line 120 (R):

    Line 122 (R):

    Line 252 (R):

    Lines 371-372 (R):

    Line 378 (R):

    Line 387 (R):

    Line 402 (IB):

    Line 403 (R):

    Line 434 (R):

    Line 457 (R):

    Line 458 (R):

    Lines 459-460 (R):

    Line 461 (R)

    Line 472 (R):

    Line 482 (R):

    Line 490 (R):

    Line 507 (IA):

    Line 510 (R):

    Line 518 (IB):

    ine 531 (R):


    Dep't of Bioorg. Chem. | Last mod.: Jul 14, 2003 | URL http://www.boc.uu.se/ | WebMaster | WWW Editor