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/
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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