求助Amber QM-MM 冻结原子问题

hhhnano

在进行QM-MM模拟冻结距离配体12埃以外的原子，设置ntr=1，不能开始模拟，如果不设置该参数，则可以正常进行，不知道什么原因？是固定原子超过250吗？还是其他原因，恳请各位高手指点。
  5.  REFERENCE ATOM COORDINATES

  defa
Error in group input::atommask.f::pop_evalstack
stack underflow




QM-MM配置文件：
Initial min of our structure QMMM
&cntrl
  imin = 1, maxcyc = 1000, ncyc = 500,
  ntx = 1,
  irest = 0,
  ntb = 0,
  cut = 12.0, ntc = 1, ntf = 1,
  ntpr = 10,
  ntwx = 1,
  ntr = 1,
  restraintmask='!(:1,2,8,9,10,11,12,13,14,15,16,18,27,29,75,78,79,80,81,82,83,84,85,86,87,90,93,108,113,120,121,122,123,124,125,126,127,128,174,180,181,182,183,184,185,186,187,197,198,199,200,201,202,209,260,261,262,263,264,265,266,268,270,273,274,275,277,285,286,290,291,292,293,294,295,296,297,298,299,300,301,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,340,607,693,950,1046,1150,1175,1422,1510,1539,1564,1733,1756,1766,1819,1899,1918,1926,1932,1957,2019,2177,2180,2192,2197,2281,2352,2378,2531,2564,2616,2690,2699,2729,2763,2773,2774,2838,2910,2958,3035,3048,3078,3139,3305,3630,3641,3756,3911,3999,4109,4199,4248,4279,4281,4420,4443,4447,4455,4471,4512,4513,4560,4566,4696,4780,4788,4808,4867,4962,4994,5021,5026,5052,5071,5093,5096,5126,5142,5146,5151,5157,5170,5177,5179,5189,5191,5204,5217,5244,5252,5257,5271,5286,5501,5536,5787,5801,5879,5883,5922,5929,6020,6063,6164,6197,6243,6325,6674,6778,6912,6951,6969,7193,7522,7606,7652,7716,7729,7732,7739,7751,7760,7806,7810,7848,7890,7891,7901,7905,7906,7910,7912,7926,7967,8017,8040,8164,8411,8421,8452,8534,8573,8603,8654,8678,8733,8774,8895,8980,9110,9131,9217,9340,9560,9572,9603)',
  restraint_wt=500.0,
  ifqnt = 1,
&end
&qmmm
qmmask=':1,12,15,122,294,295,8573'
  qmcharge = 0,
  spin = 2,
  qm_theory = 'EXTERN',
  qmshake= 0,
  qm_ewald=1, qm_pme=1,
  qmcut = 12.0,
  writepdb= 1
&end
&gau
executable = 'g16',
method = 'B3LYP',
basis = '6-31G*',
num_threads = 28,
mem = '50GB'
dipole = 1,
use_template = 0,
&end

chenjinfeng850

你可以尝试一下用距离关键词来做选择，AMBER20 手册上412页有相关的语法介绍。

hhhnano

chenjinfeng850 发表于 2020-7-15 18:08
你可以尝试一下用距离关键词来做选择，AMBER20 手册上412页有相关的语法介绍。

多谢，问题解决。

':1 < @12.0'