From: John Smith <ddfd09.gmail.com>
Date: Wed, 11 Jun 2014 12:31:29 +0100

Hi AMBER users,

Could you please help me with the command for running QM based binding
energy calculation. I have a prmtop file for the solavted complex, a prmtop
file for the complex, a prmtop file for the protein on its own and the
ligand on its own. The iput file I am using is:

startframe=1, endframe=200, interval=5,
ifqnt=1, qmcharge=0, qm_residues='123, 432'
qm_theory='PM3', qmcharge_lig=1, qmcharge_rec=-1
igb=5, saltcon=0.100,

I know that it requires a *sander *functionality but I could not implement
this into the command.

I am also trying to run nmode binding energy calculation using the same
prmtop files mentioned above and the following inout file:

   endframe=200, keep_files=2,
   nmstartframe=1, nmendframe=200,
   nminterval=5, nmode_igb=1, nmode_istrng=0.1,

The calculation takes hours and then stops recording an error in the prmtop
file for the non-solvated complex. I have used these exact prmtop file to
run ordinary GB and PB free energy calculations and they are working fine
for me.

Best regards,
Mahmood Jasim
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Received on Wed Jun 11 2014 - 05:00:02 PDT
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