Dear Amber users
I ran an easy and short minimization of the 6-aminopurine-PknG kinase complex, but something went wrong.
I parametrized the 6-aminopurine using antechamber and then i parametrized the 6-aminopurine-PknG kinase complex ( i followed all the steps described in the abtechamber tutorial).
Ones i obtained the prmtop anc inpcrd files for the complex i ran a short minimization in vacuum and without periodicity:
Initial minimisation of PknG-Adenine complex
&cntrl
imin=1,
maxcyc=500,
ncyc=250,
ntb=0,
igb=0,
cut=12
/
When i saved the pdb file after the minimization, the 6-aminopurine has lost is planarity.
Can someone help me to understand why?
I do not know if i made mistakes during the parametrization part or during the minimization step.
Thank you so much
Valentina
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Received on Wed Apr 23 2014 - 09:30:02 PDT
