On Mon, 2014-03-24 at 16:17 +0000, John Smith wrote:
> 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
> /
qmmask is not a valid mask. See Appendix C of the Amber manual for
details about the mask syntax. (I think you meant ':123,432')
Also, putting commas after every variable in the input file might
prevent these kinds of errors with some compilers.
> 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?
No. The time-consuming part is the QM/MM part, anyway, so GPU
acceleration would not buy much speed enhancement. Semi-empirical QM/MM
is not well-suited for GPU acceleration (and only mopac can do it right
now, AFAIK).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 24 2014 - 10:00:03 PDT
