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标题: 使用chemdraw和chem3D绘图+Gaussian优化不收敛 [打印本页]

作者
Author: milk_q 时间: 2024-11-6 10:25
标题: 使用chemdraw和chem3D绘图+Gaussian优化不收敛
求助各位大神，我的结构比较复杂，先用chemdraw画的，然后chem3D显示的原子结构，最后在Gaussian中几何优化，但是一直不收敛，大家能看一下是哪里的问题吗
(, 下载次数 Times of downloads: 1)
(, 下载次数 Times of downloads: 1)
这是输入文件
%nprocshared=16
%mem=20GB
%chk=PPP6-Dex2_L1.chk
#p PBE1PBE/def2svp opt freq

PPP6-Dex2_L1

0 1
H       -43.27200       5.43700       6.13900
H       -40.92900       5.90800       6.85600
H       -40.00800       5.90800       4.66800
H       -41.05700       4.80600       4.13300
H       40.54400       7.05600    -18.63700
H       40.88000       7.29000    -20.40900
H       38.10400       7.36500    -19.05900
H       39.54500       9.33100    -18.52600
H       42.88500       4.33900    -23.86300
H       41.77500       2.19300    -22.32400
H       41.99700       -1.05800    -22.52200
H       42.73600       0.31600    -22.11000
H       41.93300       5.95200    -25.37300
H       42.18000       4.33300    -26.16300
H       39.59400       6.01800    -26.24200
H       41.46400       6.96500    -27.59600
H       39.54300       5.46900    -29.24600
H       40.45000       -0.98900    -24.26600
H       42.54600       -0.89000    -26.53000
H       42.37600       -2.20500    -25.28600
H       42.14700       -2.55000    -28.33900
H       41.97700       -3.86500    -27.09500
H       39.83000       -4.30700    -27.90100
H       -44.18600       16.09700       23.24600
H       -46.71300       16.29300       23.08700
H       -50.56500       17.91200       21.40600
H       -46.54800       14.53800       20.56700
H       -47.95200       14.09800       23.28500
H       -47.94500       18.56900       22.65700
H       -43.64000       19.71500       22.10300
H       -42.60800       17.82200       23.08000
H       -49.26600       15.49200       23.85800
H       -45.82900       17.75900       23.92900
H       -44.79600       19.24800       23.79200
H       -52.71500       12.04900       21.58000
H       -53.54100       12.32200       19.98400
H       -49.84000       11.58600       17.94300
H       -49.01400       11.31300       19.54000
H       -41.24700       18.17200       21.06300
H       -41.35600       16.40600       21.48000
H       42.96100       17.85300    -21.75100
H       42.88400       19.63600    -21.78000
H       40.85800       17.02300    -20.59400
H       38.02700       16.61000    -17.11500
H       37.99800       18.69700    -22.36200
H       38.77300       17.08900    -22.03100
H       40.81700       16.24800    -18.08800
H       44.96200       17.92700    -18.48200
H       38.42100       15.67600    -20.65500
H       39.89600       15.67700    -19.59300
H       42.47400       16.14300    -20.08700
H       44.05100       16.17100    -19.18500
H       34.03200       16.00000    -20.55700
H       37.68200       13.95200    -20.13600
H       35.90600       11.75200    -18.89600
H       36.24100       11.98600    -20.66800
H       45.21900       20.32800    -21.75600
H       44.44700       20.96500    -20.23900
H       -42.80400       -4.63000       7.21600
H       -42.43100       -3.13900       6.24400
H       -39.45000       -0.83000       8.92700
H       -39.88600       -2.32800       9.86000
H       -38.50300       -2.24300       7.10100
H       -38.21800       -5.75100       7.23000
H       -36.81600       -4.98000       9.14400
H       -34.89000       -2.03100       9.15100
H       -33.13100       -3.77700       8.85700
H       -33.92100       -3.35800       7.27400
H       -31.27300       -6.17500       7.67800
H       -32.25300       -6.18300       9.21000
H       -30.78300       -4.81300       10.15600
H       -28.56700       -4.96500       9.02000
H       -28.64800       -6.37000       6.51900
H       -26.69200       -7.30500       7.75500
H       -25.77400       -4.44500       9.59400
H       -26.23200       -6.05700       10.29800
H       -24.45600       -9.08700       7.28500
H       -24.05300       -7.44500       6.61900
H       -23.12400       -8.58200       9.33500
H       -21.21800       -5.66000       9.81100
H       -20.17600       -6.71700       7.80500
H       -19.86600    -10.19000       7.30900
H       -17.52800       -9.56000       7.91300
H       -18.55900       -9.77800       9.39400
H       -14.87600       -8.54100       9.50100
H       -15.59600       -7.84200       7.98500
H       -14.86300       -9.59100       6.83100
H       -12.94500    -10.68400       7.99500
H       -12.58100       -9.79500       10.69900
H       -10.31300       -9.73700       9.65900
H       -10.68300    -12.38300       7.36500
H       -10.26800    -10.66400       6.94300
H       -7.55400       -9.32800       10.44600
H       -8.03000    -11.04200       10.82400
H       -6.43800    -10.10100       8.35100
H       -6.09100    -13.47300       7.39700
H       -4.85900    -13.34800       9.56400
H       -3.00200    -10.55900       10.65100
H       -1.18900    -12.13300       9.96700
H       -1.86100    -11.23400       8.53700
H          0.80500    -14.04800       8.25000
H       -0.29000    -14.53200       9.61800
H          1.07100    -13.53600       11.06200
H          3.37300    -13.33300       10.11900
H          3.51700    -13.88100       7.30500
H          5.39000    -15.16600       8.33900
H          6.10100    -13.03300       11.05000
H          5.62200    -14.78300       11.17400
H          7.69300    -16.72100       7.51800
H          8.11200    -14.95400       7.43400
H          8.84900    -16.89100       9.72200
H       10.65100    -14.27500       11.24300
H       11.86800    -14.65300       9.09800
H       12.28800    -17.79600       7.56400
H       13.70100    -15.91700       6.72400
H       11.93300    -15.49900       6.65500
H       14.77000    -12.99600       5.76600
H       15.41100    -14.02000       7.12500
H       16.32000    -15.40900       5.65000
H       16.68400    -14.26700       3.46100
H       15.34700    -11.73600       3.24500
H       17.67400    -11.34100       2.43400
H       18.35100    -14.53100       1.10500
H       19.30400    -13.70300       2.41400
H       19.21800       -9.25300       1.14800
H       18.25200    -10.13700       -0.11300
H       21.23600    -10.58700       0.53800
H       21.38100    -12.89200       -2.12100
H       20.85600    -10.72900       -3.25000
H       22.07400       -7.58900       -2.22100
H       23.48300       -8.03800       -4.23200
H       24.14600       -8.87200       -2.75900
H       25.63100       -9.30200       -6.32500
H       23.83400       -9.13700       -6.54600
H       24.07000       -6.94600       -6.82800
H       26.38800       -6.39000       -7.56600
H       28.23700       -8.56900       -7.29900
H       28.61200       -7.64200       -9.58600
H       27.79100       -4.27500       -8.96400
H       26.98400       -5.35600    -10.18300
H       30.46800       -7.94400    -11.79000
H       30.54500       -6.15000    -12.07900
H       31.36700       -7.61100       -9.48600
H       32.43900       -4.51900       -8.18500
H       33.95000       -4.88800    -10.13600
H       35.14600       -8.03400    -11.17400
H       36.25900       -6.01700    -12.13400
H       34.46400       -5.98400    -12.42200
H       36.85100       -3.07100    -13.38600
H       37.51300       -3.77400    -11.84500
H       38.83900       -5.10900    -13.02400
H       39.23100       -4.18200    -15.30800
H       37.46600       -2.02500    -15.99400
H       39.75200       -1.25700    -16.63500
H       41.18300       -4.37200    -17.44100
H       41.79800       -3.21700    -16.17800
N       -44.86600       3.49000       16.35800
C       -46.10300       3.35400       15.63700
C       -45.92400       3.86900       14.23000
N       -46.97400       3.84100       13.35200
C       -46.80200       4.33600       12.00000
O       35.67700       15.70900    -19.35100
C       35.66200       14.38300    -19.52900
C       42.96800       16.42400    -19.13100
C       34.41300       17.72300    -19.32400
C       36.38600       17.65900    -17.88300
C       44.18500       18.59000    -18.92400
C       -45.72500       3.53900       11.30500
N       -45.38700       3.82900       10.01100
C       -44.35200       3.06400       9.34300
C       -44.75000       1.60900       9.29800
N       -43.92300       0.69000       8.71200
C       -44.30600       -0.70800       8.66900
C       -47.84700       16.87800       21.32400
C       -49.09300       14.72500       21.56900
C       -45.32400       16.85500       21.53500
F       -48.20200       13.75100       21.55800
C       -41.92600       17.29200       21.12100
C       -52.62400       12.52700       20.57900
O       -51.50700       12.00300       19.91200
C       -51.64700       10.68200       19.75800
C       -50.57000       9.88400       19.06500
C       37.62300       17.15400    -17.98200
C       -49.44200       10.81500       18.64100
O       -47.37600       10.57300       17.53100
C       -45.33900       18.34300       21.90200
C       -47.81200       18.40400       21.56500
C       -43.21800       -1.51100       7.96800
O       -43.58900       -2.86300       7.92600
C       41.14500       -0.08200    -18.47200
C       40.95300       1.31600    -17.89900
N       41.10600       2.29700    -18.95600
O       -8.95200    -10.18100       9.19600
C       -7.81700    -10.31700       10.00700
O       -11.55900    -10.92500       8.52700
C       -10.46200    -11.37400       7.77800
O       -16.13500       -9.77800       8.44000
C       -15.04800    -10.26200       7.69900
C       40.97600       3.63100    -18.67600
C       41.13500       4.65100    -19.77600
N       41.41900       3.97500    -21.02700
C       -47.19000       4.15900       16.33700
C       -46.78800       5.62700       16.38000
C       -47.87500       6.43200       17.08000
C       45.09100       20.16200    -20.66300
O       35.49600       19.72600    -18.53500
H       41.73000       19.74800    -19.69200
O       -31.79900       -4.33100       8.43000
C       -30.61900       -4.29500       9.18600
C       -36.68200       -4.52500       8.13700
O       -36.37000       -3.16600       8.27600
C       -35.18000       -3.09700       9.01500
C       -34.07500       -3.83200       8.26900
O       -22.65900       -6.66600       8.73800
O       -34.43900       -5.17400       8.09600
O       -27.22900       -5.49800       8.58400
O       33.39600       18.36600    -19.43200
O       34.62800       13.82100    -19.79900
C       -47.47300       7.90000       17.12400
N       -48.50800       8.66600       17.79000
O       -44.85400       4.30600       13.87800
C       -48.11200       4.19100       11.23700
C       -48.58400       5.56200       10.77100
C       -49.89300       5.41700       10.00800
C       -50.36500       6.78800       9.54200
N       -51.60200       6.65100       8.82100
O       -45.16100       2.64600       11.89100
C       -44.17300       3.58400       7.92300
C       -42.74300       4.07600       7.73800
C       -42.56400       4.59600       6.31800
C       -41.13500       5.08800       6.13300
N       -40.96600       5.57900       4.79200
O       -45.80000       1.25500       9.78100
O       40.73300       3.99000    -17.54900
C       39.84700       5.45200    -19.91400
C       40.13600       6.92700    -19.66500
C       38.84800       7.72800    -19.80300
C       39.13700       9.20200    -19.55400
N       37.91100       9.96500    -19.68600
C       41.60400       4.70200    -22.17200
C       -3.25800    -11.52700       10.16400
C       -2.08200    -11.99600       9.31700
O       17.27200    -13.36100       2.41300
C          9.07400    -16.04200       9.04000
O       14.30100    -15.00100       5.69300
O          9.31900    -14.88700       9.79600
C       10.41700    -15.16800       10.62100
C       11.62400    -15.51500       9.76000
O       11.33100    -16.63900       8.97400
C          2.48700    -13.16800       9.46500
O          2.17400    -14.35700       8.79300
O       -2.40400    -13.21500       8.70300
C       -1.28800    -13.59200       7.94200
C       -0.08000    -13.74900       8.85500
C       41.90000       3.99900    -23.47300
N       41.93700       2.56600    -23.25100
C       42.19000       1.71800    -24.29600
C       42.22900       0.22700    -24.06500
N       41.97100       -0.05000    -22.67700
O       41.53000       5.90800    -22.14000
O       21.77400       -9.58400       -1.80400
C       22.00200       -8.56800       -2.74400
O       24.69000       -7.92000       -5.12100
C       24.90100       -6.92500       -6.08700
O       26.18500       -8.43500       -7.42200
C       27.42200       -8.61000       -8.05700
C       40.81100       4.32700    -24.48600
C       41.43200       5.01200    -25.69600
C       40.34300       5.34000    -26.70900
C       40.96300       6.02500    -27.91900
N       39.93500       6.33500    -28.87600
O       42.38300       2.16300    -25.40200
C       41.16600       -0.44600    -24.92200
C       41.83000       -1.43300    -25.87400
C       40.76700       -2.10600    -26.73100
C       41.43100       -3.09300    -27.68200
N       40.42700       -3.72900    -28.49200
C       -44.01500       16.38000       22.18400
C       -46.47400       19.05200       21.16600
C       -50.01400       14.06200       20.85300
C       -46.62800       16.18300       21.98300
C       -49.15500       16.21600       21.82000
O       35.70900       17.47600    -16.72300
C       30.40900       -6.94200    -11.30900
C       31.50400       -6.82000    -10.25700
C       32.45700       -5.50800       -8.69600
C       33.80100       -5.69700       -9.38700
C       35.08000       -7.05700    -10.64500
C       35.26200       -5.92500    -11.64800
C       35.35200       -3.69600    -11.95400
C       36.71400       -3.86200    -12.61500
C       29.14200       -5.51600    -10.11300
C       38.05800       -5.21600    -13.81000
C       38.22300       -4.10800    -14.84200
C       38.24800       -1.88800    -15.21300
C       39.62600       -2.02900    -15.84400
C       41.03500       -3.37200    -16.97400
C       41.18400       -2.29100    -18.03600
H       -44.98600       3.14200       17.30900
H       -44.16400       2.87400       15.94700
C       -50.39900       16.83800       21.23700
O       -46.34200       19.97300       20.39400
H       -47.87000       3.47400       13.64700
H       -44.43600       -1.08800       9.70700
H       -43.08800       -1.13100       6.93000
C       -4.65600    -12.60100       8.76400
H       41.97500       5.33800    -19.52600
H       41.48100       2.96500    -21.05300
H       -47.32200       3.77900       17.37500
H       -45.83100       5.73200       16.93900
H       -48.83200       6.32600       16.52100
H       -48.00700       6.05200       18.11800
H       -47.34100       8.27900       16.08600
H       -49.33600       8.20100       18.13900
H       41.71500       1.50100    -17.10900
H       -48.88100       3.74000       11.90300
H       -50.52300       7.44600       10.42600
H       -51.91700       7.57000       8.51000
H       -51.43700       6.13200       7.95900
H       -44.88000       4.42500       7.74400
H       -42.53700       4.89600       8.46200
C       -46.61700       14.67800       21.66900
C       -47.90500       14.02000       22.17600
H       -40.42800       4.24700       6.31200
H       38.44000       7.59900    -20.83100
H       43.23300       -0.16500    -24.34100
H       39.84200       4.40000    -27.03200
H       40.62000       0.32500    -25.51000
H       40.87200       -4.39000    -29.12900
H       -45.74200       14.20600       22.17000
H       -43.74900       18.98300       20.49200
H       -46.56600       19.33000       23.38900
H       -52.29900       17.77600       20.33400
H       36.12200       19.00100    -21.10700
H       40.07600       17.39500    -16.84400
H       38.29200       15.14600    -18.92100
H       37.34700       13.71900    -18.36400
H       36.34200       20.09200    -18.34500
H       -37.69600       -2.59100       8.69200
H       -35.33400       -3.57000       10.01000
H       -30.33200       -3.23600       9.37400
H       -27.68900       -7.38400       9.27300
H       -22.11000       -8.43300       7.83300
H       -19.45800       -8.51800       6.72200
H       -15.27500    -11.28900       7.33500
H       -11.01700       -8.97000       8.16800
H       -5.75100    -10.93400       9.81400
H       -3.47900    -12.28900       10.94500
H          1.55000    -11.79400       10.85200
H          4.27900    -15.71300       9.67100
H          9.97400    -16.28300       8.43100
H       13.33400    -17.11100       8.88500
H       15.32000    -16.16600       4.33400
H       18.32500    -12.30300       3.83300
H       20.57800       -9.68800       -0.89800
H       21.16000       -8.54000       -3.47100
H       24.93200       -5.92900       -5.59200
H       26.81500       -7.54300       -9.84100
H       32.49800       -6.94000    -10.74200
H       35.87800       -6.99800       -9.87100
H       38.16500       -6.20500    -14.30800
H       40.40800       -1.89200    -15.06300
C       36.64900       12.11500    -19.64100
C       38.79600       15.84900    -19.62100
C       42.80800       17.92000    -18.89500
C       -43.06200       17.59000       22.09100
C       39.84800       17.98300    -18.92300
C       43.05100       18.76100    -21.11400
C       39.90800       18.80800    -21.32800
H       39.62000       19.01200    -18.56500
H       -45.31400       16.60200       20.45100
C       -51.21700       14.70100       20.22500
O       -6.98100    -12.07000       8.61500
C       -12.37600       -9.10800       9.84700
C       -16.93600       -7.90200       9.68500
C       -41.25600       -3.36600       8.04800
C       -19.63300       -9.14800       7.62300
C       -26.05700       -5.49500       9.35400
C       -20.36100       -7.32200       8.72000
C       -11.22100       -9.65600       9.02000
O       -29.86400       -6.32700       8.18100
O       -40.94100       -2.00200       8.12100
C          3.29900    -14.69800       8.02800
O       13.02600    -14.58300       8.14100
C       24.66100       -9.14600       -5.80200
O       18.85800    -11.24900       1.51200
C       15.46600    -15.25300       4.95400
O       20.24300    -11.72100       -0.86600
C          7.05600    -14.34100       9.61300
C       21.44600    -11.93700       -1.55300
C       24.43500    -10.27500       -4.80500
O       27.60600       -6.25800       -8.43900
H       -43.39500       3.16900       9.90100
H       40.38300       -0.26700    -19.26200
H       -49.73600       4.75900       9.12400
H       39.43900       5.32300    -20.94200
H       39.10300       5.08900    -19.17000
H       39.88100       9.56500    -20.29800
H       37.04400       9.49400    -19.91200
H       40.31000       3.38700    -24.80900
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H       -21.68200       -7.30300       10.43600
H       -19.43900       -7.34700       9.34300
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H       42.20200       -2.34500    -18.48100
H       40.42100       -2.44600    -18.83200
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C       34.38600       16.22800    -19.52700
C       35.71100       18.41600    -18.98700
C       44.43400       18.80800    -20.42900
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C       18.72600    -12.42700       0.76300
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H       -45.85900       4.57700       9.52000
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H       42.16400       -0.16600    -18.91100
H       39.93400       1.40000    -17.46000
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H       -46.65600       6.00600       15.34200
H       -46.51600       8.00500       17.68200
H       -47.95400       3.53300       10.35200
H       -48.74100       6.21900       11.65500
H       -47.81400       6.01200       10.10500
H       -50.66300       4.96600       10.67400
H       -49.59600       7.23900       8.87600
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H       -42.03600       3.23500       7.91700
H       -42.77100       3.77600       5.59400

报错信息

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作者
Author: cokie 时间: 2024-11-6 12:34
这种巨柔性的体系，你起码得做构象搜索，之后再用量化得到能量最低的几个构象才有意义。
而且本身这种大体系直接优化就很难收敛，即使你做了构象搜索之后，最好也是从半经验 — 小基组 — 大基组这样一个顺序得到最终结构才会比较稳当。

最后就是这种超级柔性体系你优化的时候肯定得用带色散矫正的泛函，得到的几何结构才有意义。即使要用PBE0，最好也是用PBE0-D3(BJ)而非像你这样直接用PBE0。

作者
Author: wal 时间: 2024-11-6 13:15
本帖最后由 wal 于 2024-11-6 13:19 编辑

你这好像连scf都没成功，而不是几何不收敛。这么大体系16核20gb真算的动dft级别几何优化吗，有点怀疑，如果你只是一轮scf就做了四个小时，那你freq得做到啥时候去啊

作者
Author: milk_q 时间: 2024-11-6 15:37

cokie 发表于 2024-11-6 12:34
这种巨柔性的体系，你起码得做构象搜索，之后再用量化得到能量最低的几个构象才有意义。
而且本身这种大体 ...

好的谢谢

作者
Author: milk_q 时间: 2024-11-7 10:31

cokie 发表于 2024-11-6 12:34
这种巨柔性的体系，你起码得做构象搜索，之后再用量化得到能量最低的几个构象才有意义。
而且本身这种大体 ...

请问cokie老师，这么大的体系设置构象旋转参数文件是不是很困难很复杂，我这个需要先把chem3D导出来到Gaussian里调整一下键长和二面角，再做构想搜索

作者
Author: Uus/pMeC6H4-/キ 时间: 2024-11-7 10:53
本帖最后由 Uus/pMeC6H4-/キ于 2024-11-7 10:59 编辑

没看懂计算目的，这个是聚合物中截取的片段吗，在溶液还是固相，构象搜索几何优化之后要做什么？推荐读一读社长博文http://sobereva.com/680，体系真这么大的话该考虑下计算方法（DFT/半经验/分子力场等等）和可用资源（核心/内存/时间等）的问题，以及能否从现在这个孤立体系改成CP2K之类做周期性体系计算。

作者
Author: milk_q 时间: 2024-11-7 11:07

Uus/pMeC6H4-/キ发表于 2024-11-7 10:53
没看懂计算目的，这个是聚合物中截取的片段吗，在溶液还是固相，构象搜索几何优化之后要做什么？推荐读一读 ...

是聚合物和药物的混合体系，要在水中，后面是用分子动力学模拟它的自组装，主要目的还是几何优化让它的能量降到极小值，目前是chemdraw画的结构，放到chem3D中，然后转换成gjf在Gaussian中优化，SCF一直不收敛，想知道这个体系究竟怎么优化它的结构

作者
Author: 霜晨月 时间: 2024-11-7 11:22
本帖最后由霜晨月于 2024-11-7 11:27 编辑

milk_q 发表于 2024-11-7 11:07
是聚合物和药物的混合体系，要在水中，后面是用分子动力学模拟它的自组装，主要目的还是几何优化让它的能 ...

1. 直接用分子力场做分子动力学，没必要先用DFT优化。可以用半经验（XTB等）做个opt+freq用来计算原子电荷和创建拓扑参数（如果需要的话）。
2. 你这个含有肽结构，有很多手性中心，但你用ChemDraw画的时候都没有标出手性构型，Chem3D自动生成的立体构型很可能有误。建议在ChemDraw中重画（标明手性构型）。

作者
Author: cokie 时间: 2024-11-7 13:56

milk_q 发表于 2024-11-7 10:31
请问cokie老师，这么大的体系设置构象旋转参数文件是不是很困难很复杂，我这个需要先把chem3D导出来到Gau ...

如果你的目的是跑动力学，那么不需要一定做DFT，如8L所讲，可以xTB 跑GFN2-xTB获得构象，很快，而且个人体验比PM7或者PM6-D3H4得到的结果可信度更高一些，之后计算原子电荷。拓扑参数用sobtop按经验生成即可，无需一定做freq。

作者
Author: milk_q 时间: 2024-11-7 14:38

霜晨月发表于 2024-11-7 11:22
1. 直接用分子力场做分子动力学，没必要先用DFT优化。可以用半经验（XTB等）做个opt+freq用来计算原子电 ...

好的谢谢

作者
Author: milk_q 时间: 2024-11-7 14:39

cokie 发表于 2024-11-7 13:56
如果你的目的是跑动力学，那么不需要一定做DFT，如8L所讲，可以xTB 跑GFN2-xTB获得构象，很快，而且个人 ...

好的谢谢

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