Subject: CHARMM: GTP and GDP parameters

From: tluchko <[email-masked]>
Date: Thu, 2 Jan 2003 14:22:07 -0700

Hello,

I am trying to come up with some parameters for GTP and GDP bound to tubulin 
for the CHARMM27 parameter set.  My hope is to use ATP and ADP as a starting 
point, however, I have run into two problems.  The first is that CHARMM does 
not seem to like the ATP/ADP parameters themselves.  I get errors such as

 <CODES>: No angle parameters for     5 ( ON6B CN7  CN8 )
 <CODES>: A TOTAL OF    5 MISSING PARAMETERS

      ***** LEVEL -1 WARNING FROM <CODES> *****
      ***** CODES> MISSING PARAMETERS
      ******************************************
      BOMLEV ( -2) IS NOT REACHED. WRNLEV IS  5

 CHECKDH> dihedral :    1   28   31   32 will NOT be generated

Is there something wrong with the parameters?  If these parameters are 
supposed to be missing for ADP/ATP why is this correct?

The second problem is with the charge distribution.  GTP/GDP binds to tubulin 
in two places in each monomer (according to the pdb).  This means removing 
four hydrogens per dimer and gives a non-integer net charge for the system.  
what methods/tools can I use to redistribute the correct charge among the 
remaining atoms?

Thank you,

Tyler
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><    Tyler Luchko                                       Masters Student    ><
><    Deparment of Physics                                  780-492-5519    ><

><    University of Alberta                          [email-masked]    ><
><    Edmonton, Alberta, Canada                                    p442a    ><
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