My apologies for forgetting to attach the .pdb and .xyz files to the previous message:
> On 11 Jul 2019, at 09:36, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
>
> Dear Amber experts,
>
> I’m starting a new thread of the same previously reported issue but changing the subject to add clarity to it.
>
> For comparison purposes with a previous study, I’m attempting to run adaptive solvent QM/MM dynamics of a system consisting in a protein-ligand complex to which a loop of another protein is docked and kept in this position by restraints applied to its borders. A Mg2+ ion is also present in the active site and I wish to treat quantum mechanically water molecules in the vicinity of the ligand (GTP). To do so, this is the input file I used:
>
> 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=10, ntwx=10, ntwr=100, ioutfm=1,
> ntc=2, ntf=2,
> noshakemask = '.176-189,474-494,521-534,900-909,917-933,2646-2689,2828-2851,2941-2946',
> ntr=1,
> restraintmask = ':170,185,@CA,C,N',
> restraint_wt=5.0,
> ifqnt=1,
> /
> &qmmm
> qmmask=':12,13,32,35,59,61,168,169,179,196-197',
> qmcharge=-1,
> adjust_q=0,
> qm_theory='PM3',
> qmshake=0,
> qmcut=8.0,
> vsolv=3,
> writepdb=1,
> /
> &vsolv
> nearest_qm_solvent_resname='WAT',
> nearest_qm_solvent=2,
> nearest_qm_solvent_fq=1,
> nearest_qm_solvent_center_id=0,
> qm_center_atom_id=2647,
> /
> &adqmmm
> n_partition=4,
> RA=7,
> RT=9,
> print_qm_coords=1,
> /
>
> From the 4 partitions that result in mdout files 000, 001, 002 and 003, mdcrd and restrt files are created for the first one (000) only. Is this behaviour normal?
>
> Aside, the simulation is stopped due to the fourth partition which mdout file displays the following error message:
>
> SANDER BOMB in subroutine nonbond_list
> volume of ucell too big, too many subcells
> list grid memory needs to be reallocated, restart sander
>
> Yet, when checking the size of the QM region through the .pdb files written thanks to the “writepdb” keyword, this region doesn’t ‘blow up’ (see attachments named qmmm_region.pdb.*). Nevertheless, when checking this same region through the .xyz files generated thanks to the “print_qm_coords” keyword (QM_coords.* files), a residue from the loop of the second protein appears to be far away, as when visualising a wrapped trajectory that hasn’t been unwrapped. Moreover, in the .xyz file corresponding to the partition that leads to the halt of the simulation (QM_coords.003.xyz <http://qm_coords.003.xyz/><http://qm_coords.xyz/ <http://qm_coords.xyz/>>), a water molecule is observed with the “wrapped” residue from the second protein such that this water molecule appears in both sides i.e. on the side of the protein-ligand complex and on the side of the second protein loop. Hence, I suspect this water molecule on “both sides” could be leading to the repeated "vlimit exceeded” messages I get before the crash:
>
> vlimit exceeded for step 156; vmax = 20.4418
> wrapping first mol.: -45.29463 -64.05628 0.00000
> vlimit exceeded for step 157; vmax = 20.3292
> wrapping first mol.: -45.54621 -64.41207 0.00000
> vlimit exceeded for step 158; vmax = 20.2651
> wrapping first mol.: -45.75854 -64.71234 0.00000
>
> Could this be the case?
>
> Any thoughts on what shall be done to pursue this adQM/MM simulation?
> Thanking you in advance for any insights on this matter,
>
> Sincerely,
>
> Ruth
>
> P.S: I’m using Amber 16 on a cluster external to the lab
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 11 2019 - 01:00:03 PDT
