[AMBER] "QMMM of protein-ligand complex: Unable to achieve self consistency" and "bond stretch too far"

From: <psu4.uic.edu>
Date: Tue, 28 Aug 2012 18:48:31 -0500

Dear Amber,

 This question is a little complicated, so let's summarize the
abbreviation of my TI-QMMM softcore potential test run first:

                             mask 0 mask 1
ligand only : TC2 => TCL
ligand + protein: TC2 with protein => TCL with protein

  ( 1.) In both "TCL" and "TCL with protein" softcore potentials
production run, a warning keeps popping out: "*QMMM of protein-ligand
complex: Unable to achieve self consistency. No convergence in SCF after
1000 steps. QMMM: Job will continue with unconverged SCF. Warning energies
QMMM: and forces for this step will not be accurate." and "* / *QMMM of
ligand : Unable to achieve self consistency* ....". I am aware that there
is the similar issue reported
before<http://archive.ambermd.org/201010/0388.html>.
However, I didn't include any water in QM regions so I am not sure what
happen on my runs. *Interestingly, the other pair of softcore potential
jobs, "TC2" & "TC2 with protein" run perfectly without this warning. *

  ( 2.) The other issue is in the softcore potentials production run of
"TCL" and "TCL with protein". *The ligand's bonds stretch too far after
about 200ps of production run.*
(movie<http://s1076.photobucket.com/albums/w454/happypsu4/?action=view&current=no_protein_step_2_TCL.mp4>)
However, such a stretch-out happens around 200 ps later than the* "QMMM of
protein-ligand complex: Unable to achieve self consistency*" warning. So
it seems like ( 1. ) & ( 2. ) might be independent issues?

  On the other hand, I originally thought this stretch-out might be due to
SHAKE failure. However, I found I turned SHAKE off in the whole softcore
potential related simulation. Then I thought it might be something wrong
with .prmtop and .inpcrd. However, in the non-softcore potential runs, the
same .prmtop and .inpcrd works pretty well and no any issue / warning. So
now I am quite confused. Could you give me some comments? The followings
are my results / input files.


                             mask 0 mask 1
ligand only : TC2 => TCL
(pressure<http://i1076.photobucket.com/albums/w454/happypsu4/TC2_solvate_33_0_1_summary_pressure.png>/
energy<http://i1076.photobucket.com/albums/w454/happypsu4/TC2_solvate_33_0_1_summary_energy.png>
/temperature<http://i1076.photobucket.com/albums/w454/happypsu4/TC2_solvate_33_0_1_summary_TEMP.png>/
RMSD<http://i1076.photobucket.com/albums/w454/happypsu4/TC2_solvate_33_0_1_summary_RMSD.png>/
movies<http://s1076.photobucket.com/albums/w454/happypsu4/?action=view&current=no_protein_step_2_TCL.mp4>
/.out<https://dl-web.dropbox.com/get/Public/warning/TCL_solvate_33_prod_v1_l1.out?w=c9525407>
/ .prmtop<https://dl-web.dropbox.com/get/Public/warning/TCL_solvate_33.prmtop?w=a56740a5>
/ .inpcrd<https://dl-web.dropbox.com/get/Public/warning/TCL_solvate_33.inpcrd?w=0fb94d48>
)
ligand + protein: TC2 with protein => TCL with protein (pressure
/energy<http://i1076.photobucket.com/albums/w454/happypsu4/FabI_NAD_TCL_wat_33A_1_1_summary_energy.png>
/temperature<http://i1076.photobucket.com/albums/w454/happypsu4/FabI_NAD_TCL_wat_33A_1_1_summary_TEMP.png>/
RMSD<http://i1076.photobucket.com/albums/w454/happypsu4/FabI_NAD_TCL_wat_33A_1_1_summary_RMSD.png>/
movies<http://s1076.photobucket.com/albums/w454/happypsu4/?action=view&current=with-FabI_step2.mp4>
/.out<https://dl-web.dropbox.com/get/Public/warning/FabI_NAD_TCL_wat_33A_prod_v1_l1.out?w=73ec51e3>/
 .prmtop<https://dl-web.dropbox.com/get/Public/warning/FabI_NAD_TCL_wat_33A.prmtop?w=32ec69ca>/
.inpcrd<https://dl-web.dropbox.com/get/Public/warning/FabI_NAD_TCL_wat_33A.inpcrd?w=d42729ec>
 )

###################################The input file of "TCL with protein"
######################################
cat << EOF > mdin_min_v0_l${X}
FabI step 1 Minimization Therm Integ${X}: protein+ligand
 &cntrl
  imin = 1,
  ntx = 1,
  maxcyc = 2000,
  ntmin = 2,
  ntpr = 100,
  ntf = 1,
  ntc = 1,
  ntb = 1,
  cut = 10.0,
  icfe = 1,
  clambda =0.0092,
EOF

cp mdin_min_v0_l${X} mdin_min_v1_l${X}

cat << EOF >> mdin_min_v0_l${X}
  ifsc=1,
  crgmask='${mask0}',
  scmask='${mask0}',
 &end
EOF
cat << EOF >> mdin_min_v1_l${X}
  ifsc=1,
  crgmask='${mask1}',
  scmask='${mask1}',
 &end
EOF

cat << EOF > mdin_equi_v0_l${X}
FabI step 1 Equilibration 1 Therm Integ${X}: protein+ligand
 &cntrl
  imin = 0,
  irest = 0,
  ntx = 1,
  ntb = 1,
  cut = 10.0,
  ntr = 1,
  ntc = 1,
  ntf = 1,
  tempi = 0.0,
  temp0 = 300.0,
  ntt = 3,
  gamma_ln = 2.0,
  nstlim = 50000,
  dt = 0.001,
  ntpr = 250,
  ntwx = 250,
  ntwr = 2500,
  icfe = 1,
  clambda =0.0092
EOF

cp mdin_equi_v0_l${X} mdin_equi_v1_l${X}

cat << EOF >> mdin_equi_v0_l${X}
  ifsc=1,
  crgmask='${mask0}',
  scmask='${mask0}',
/
Keep the Protein fixed with weak restraints
10.0
RES 1 258
/

END
END
EOF

cat << EOF >> mdin_equi_v1_l${X}
  ifsc=1,
  crgmask='${mask1}',
  scmask='${mask1}',
/
Keep the Protein fixed with weak restraints
10.0
RES 1 258
/

END
END
EOF

cat << EOF > mdin_equi_v0_2${X}
FabI step 1 Equilibration 2 Therm Inter protein ligand
 &cntrl
  imin = 0,
  irest = 1,
  ntx = 5,
  ntb = 2,
  ntp = 1,
  pres0 = 1.0,
  taup = 2.0,
  cut = 10,
  ntr = 0,
  ntc = 1,
  ntf = 1,
  tempi = 300.0,
  temp0 = 300.0,
  ntt = 3,
  gamma_ln = 2.0,
  nstlim = 50000,
  dt = 0.001,
  ntpr = 250,
  ntwx = 250,
  ntwr = 2500,
  icfe = 1,
  clambda =0.0092,
EOF

cp mdin_equi_v0_2${X} mdin_equi_v1_2${X}

cat << EOF >> mdin_equi_v0_2${X}
  ifsc=1,
  crgmask='${mask0}',
  scmask='${mask0}',
 &end
EOF

cat << EOF >> mdin_equi_v1_2${X}
  ifsc=1,
  crgmask='${mask1}',
  scmask='${mask1}',
 &end
EOF

cat << EOF > mdin_prod_v0_l${X}
NPT production
 &cntrl
  imin = 0,
  ntx = 5,
  irest = 1,
  ntpr = 250,
  ntwr = 2500,
  ntwx = 250,
  ntf = 1,
  ntc = 1,
  ntb = 2,
  cut = 10.0,
  nstlim = 600000,
  dt = 0.001,
  temp0 = 300.0,
  ntt = 3,
  gamma_ln = 2.0,
  ntp = 1,
  pres0 = 1.0,
  taup = 2.0,
  icfe = 1,
  clambda =0.0092,
EOF

cp mdin_prod_v0_l${X} mdin_prod_v1_l${X}

cat << EOF >> mdin_prod_v0_l${X}
  ifsc=1,
  crgmask='${mask0}',
  scmask='${mask0}',
  ifqnt = 1
  /
  &qmmm
  iqmatoms=3868,3869,3870,3871,3872,
           3873,3874,3875,3876,3877,
           3878,3879,3880,3881,3882,
           3883,3884,3885,3886,3887,
           3888,3889,3890,1395,1394,
           1396,1398,1399,2328,2327,
           3833,3834,3835,3836,3837,
           3838,3839,3840,3841,3862,
           3863,3864,3865,3866,3867
  qmcharge=-1,
  qm_theory='PM3',
  qmshake=0,
  qm_ewald=1, qm_pme=1
 /

 &end
EOF
cat << EOF >> mdin_prod_v1_l${X}
  ifsc=1,
  crgmask='${mask1}',
  scmask='${mask1}',
  ifqnt = 1
  /
  &qmmm
  iqmatoms=3868,3869,3870,3871,3872,
           3873,3874,3875,3876,3877,
           3878,3879,3880,3881,3882,
           3883,3884,3885,3886,3887,
           3888,3889,3890,1395,1394,
           1396,1398,1399,2328,2327,
           3833,3834,3835,3836,3837,
           3838,3839,3840,3841,3862,
           3863,3864,3865,3866,3867
  qmcharge=-1,
  qm_theory='PM3',
  qmshake=0,
  qm_ewald=1, qm_pme=1
 /
 &end
EOF

   Best,
   Pin-Chih
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Received on Tue Aug 28 2012 - 17:00:02 PDT
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