[AMBER] set RA, RT and n_partition in adQM/MM run

From: Ruth Helena Tichauer <rhtichau.laas.fr>
Date: Wed, 15 May 2019 12:57:38 +0200

Dear Amber experts,

I’m trying to run adaptive solvent QM/MM dynamics of a protein ligand complex containing a Mg2+ ion in the reactive region and that is treated quantum mechanically.

I wish water molecules within 5A of an atom from the QM region (atom 2647) to be treated quantum mechanically during the run, so I set RA=5. As from previous calculations I have estimated that “exchange” happens between this distance and 7A, I have set RT=7.

Now, while running these simulations with the following input:

&cntrl
imin=0,
irest=1, ntx=5,
ntb=2, pres0=1.0, ntp=1, taup=1.0,
cut=12.0,
temp0=300.0,
ntt=3, gamma_ln=2.0, ig=-1,
nstlim=50000, dt=0.001,
ntpr=250, ntwx=200, ntwr=500, ioutfm=1,
ntc=2, ntf=2,
ntr=1,
restraint_wt=5.0,
ifqnt=1,
/
&qmmm
qmcharge=-1,
qm_theory='PM3',
qmshake=0,
qmcut=8.0,
vsolv=3,
/
&vsolv
nearest_qm_solvent_resname='WAT',
nearest_qm_solvent=4,
nearest_qm_solvent_fq=1,
nearest_qm_solvent_center_id=0,
qm_center_atom_id=2647,
/
n_partition=8,
RA=5,
RT=7,
print_qm_coords=1,
/

I get the following error message:

Radius of QM region is smaller than the first partition.
Reduce the number of solvent molecules in the active region or increase RA

But for an other system, using the following input (same values for RA, RT as you may see because the reaction center is absolutely identical):

&cntrl
imin=0,
irest=1, ntx=5,
ntb=2, pres0=1.0, ntp=1, taup=1.0,
cut=12.0,
temp0=300.0,
ntt=3, gamma_ln=2.0, ig=-1,
nstlim=50000, dt=0.001,
ntpr=250, ntwx=200, ntwr=500, ioutfm=1,
ntc=2, ntf=2,
ifqnt=1,
/
&qmmm
qmcharge=-1,
qm_theory='PM3',
qmshake=0,
qmcut=8.0,
vsolv=3,
/
&vsolv
nearest_qm_solvent_resname='WAT',
nearest_qm_solvent=5,
nearest_qm_solvent_fq=1,
nearest_qm_solvent_center_id=0,
qm_center_atom_id=2647,
/
n_partition=8,
RA=5,
RT=7,
print_qm_coords=1,
/

I get the following error message:

Radius of T region is larger than the biggest partition.
Increase the number of partitions or reduce RT.

So I wonder, how should I set RA and RT values (and the number of partitions as well) so that water molecules within 5A of the desired atom (2647) are treated quantum mechanically and their nature becomes MM at distances of 7A from this same atom?

Thank you in advance for any insight into this matter.

Sincerely yours,

Ruth
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Received on Wed May 15 2019 - 04:00:01 PDT
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