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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:

Constant Temp 300K adQM/MD simulation

&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,

noshakemask = '.176-189,474-494,521-534,900-909,917-933,2646-2689,2828-2851',

ntr=1,

restraintmask = ':170,185,.CA,C,N',

restraint_wt=5.0,

ifqnt=1,

/

&qmmm

qmmask=':12,13,32,35,59,61,168,169,179',

qmcharge=-1,

adjust_q=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,

/

&adqmmm

n_partition=8,

RA=5,

RT=7,

print_qm_coords=1,

/

I get the following error message:

SANDER BOMB in subroutine adaptive_qmmm (qmmm_adaptive_module)

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):

Constant Temp 300K adQM/MD simulation

&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,

noshakemask = '.176-189,474-494,521-534,900-909,917-933,2646-2689,3859-3882',

ifqnt=1,

/

&qmmm

qmmask=':12,13,32,35,59,61,168,169,241',

qmcharge=-1,

adjust_q=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,

/

&adqmmm

n_partition=8,

RA=5,

RT=7,

print_qm_coords=1,

/

I get the following error message:

SANDER BOMB in subroutine adaptive_qmmm (qmmm_adaptive_module)

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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AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

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

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:

Constant Temp 300K adQM/MD simulation

&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,

noshakemask = '.176-189,474-494,521-534,900-909,917-933,2646-2689,2828-2851',

ntr=1,

restraintmask = ':170,185,.CA,C,N',

restraint_wt=5.0,

ifqnt=1,

/

&qmmm

qmmask=':12,13,32,35,59,61,168,169,179',

qmcharge=-1,

adjust_q=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,

/

&adqmmm

n_partition=8,

RA=5,

RT=7,

print_qm_coords=1,

/

I get the following error message:

SANDER BOMB in subroutine adaptive_qmmm (qmmm_adaptive_module)

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):

Constant Temp 300K adQM/MD simulation

&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,

noshakemask = '.176-189,474-494,521-534,900-909,917-933,2646-2689,3859-3882',

ifqnt=1,

/

&qmmm

qmmask=':12,13,32,35,59,61,168,169,241',

qmcharge=-1,

adjust_q=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,

/

&adqmmm

n_partition=8,

RA=5,

RT=7,

print_qm_coords=1,

/

I get the following error message:

SANDER BOMB in subroutine adaptive_qmmm (qmmm_adaptive_module)

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

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

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