Hi AMBER users
I am trying to run a QM/MM MD simulation on a protein ligand complex (431
amino acid protein). I used Antechamber initially for the prepin and frcmod
files. I then used xLeap to generate the prmtop and inpcrd files. I am
trying to run a QM/MM simulation where the quantum region would include the
ligand and a key residue in the protein (CYS123). I am using AMBER12 and
have a GPU machine. I noticed that I cannot use the PMEMD to run QM/MM and
I have to use Sander, even with Sander I am getting the error message
"Internal namelist read error" and the calculation stops. The input files
is as follows:
Initial minimisation
&cntrl
imin=1, maxcyc=2000, ncyc=1000,
cut=12, ntb=1, igb=0, ifqnt=1
/
&qmmm
qmmask = '123, 432'
qmcharge = 0,
qm_theory = 'PM3'
qmcut = 12.0
/
END
END
This input file is for the initial minimisation and I was planning to use
the QM part on the MD stages as well but unfortunately I am being unable to
progress because of the aforementioned error message.
Could you please help me with that?
Also is there a command that I can use to run the calculations on the GPU?
Many thanks
Mahmood Jasim
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Received on Mon Mar 24 2014 - 09:30:02 PDT
