[gmx-users] Makeing CPMD_int.run

[Mahnam]

In God We Trust
Hello Dr Biswas 
Thank you very much for your reply.
We are working with Gromos force field by QMMM_GMX for QMMM minimization of 
bilirubin at HSA.
1-How can we add non-polar hydrogens to united atoms in QM box of  
bilirubin?
2-How can we make CPMD_int.run and in section atoms and how can we calculate 
coordinates for each atoms for bilirubin molecule?  
3-May I ask you to explain  EXTELEC section in your examples? 
4-It seems that QM box at your examples is more than space between the 
outermost atoms  plus 3 angstrom?. How can we select QM box dimensions for 
bilirubin?       
Thank you very much in advance..
Sincerely yours
Karim Mahnam
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University 
P.O.box 13145-1384
Tehran 
Iran 
http://www.ibb.ut.ac.ir/
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