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muxiachuixue木虫 (正式写手)
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[求助]
求助如何固定原子坐标进行优化，快搞疯了
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小弟算一个酶催化反应的过渡态，第一步是优化反应模型（65个原子，C/H/O/N/P），氨基酸残基坐标来自晶体结构，配体分子是我随便摆的，现在想固定氨基酸残基截断点的坐标，防止优化过程中氨基酸变化过大，于是将要固定的原子前加-1，opt，出现如下错误： New curvilinear step failed, DQL= 2.27D-05 SP=-1.06D-01. OIter 1 Iteration 1 Try 1 RMS(Cart)= 1.33837418 RMS(Int)= 0.10615517 OIter 1 Iteration 2 Try 1 RMS(Cart)= 0.48462652 RMS(Int)= 0.03868199 OIter 1 Iteration 3 Try 1 RMS(Cart)= 0.14237191 RMS(Int)= 0.02029609 OIter 1 Iteration 4 Try 1 RMS(Cart)= 0.14305967 RMS(Int)= 0.02619501 Old curvilinear step not converged, using linear step OIter 1 Iteration 1 Try 1 RMS(Cart)= 0.00160751 RMS(Int)= 0.00012488 OIter 1 Iteration 2 Try 1 RMS(Cart)= 0.00068394 RMS(Int)= 0.00002980 OIter 1 Iteration 3 Try 1 RMS(Cart)= 0.00013829 RMS(Int)= 0.00002363 OIter 1 Iteration 4 Try 1 RMS(Cart)= 0.00015263 RMS(Int)= 0.00002022 Old curvilinear step not converged, using linear step Error imposing constraints Error termination via Lnk1e in /home/g09c01/g09/l103.exe at Sat Feb 18 05:51:33 2012. Job cpu time: 5 days 5 hours 52 minutes 14.6 seconds. 而且我查看优化过程中的几个中间结构，发现其实固定的几个原子相对位置都变了！ 于是尝试加opt=cartesian；优化了100多步，没优化完，也没出现错误，但是查看坐标相对位置，固定的几个原子相对位置还是变了，虽然变化很小！ 现在尝试用内坐标加modredundant，不知可否。问两个问题： 1.如何成功地固定原子进行优化？ 2.没优化完的结构打开来看，出现如下错误，提示电荷与自旋多重度不匹配？我设的电荷-4，自旋多重度1，没错啊~不理解；以下附上gjf和out，望大侠不吝赐教！  [ Last edited by muxiachuixue on 2012-2-18 at 19:25 ] |
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2012-02-18 19:21:39, 4.92 K
2012-02-18 19:21:41, 441.3 K
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15楼2014-07-17 01:37:19
muxiachuixue
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gjf文件 %nprocshared=12 %mem=4000MB # opt=cartesian freq b3lyp/6-31+g(d,p) geom=connectivity initial1_opt+freq_cartesian -4 1 C -7.41401000 -0.97994100 -3.21093900 C -6.61418700 -0.53885300 -2.02537000 N -7.17639100 -0.33652000 -0.78298000 C -5.27034800 -0.25665100 -1.86879000 C -6.17035100 0.02671300 0.05746700 N -4.99945100 0.09614400 -0.56085800 C -11.88427500 -0.99792700 0.87376500 C -11.08435300 -0.60518200 -0.38621300 O -9.83345600 -0.46883100 -0.20041400 O -11.73247900 -0.42804500 -1.43980900 O 1.70337200 -4.66185600 -1.05342000 C 2.22561200 -4.36144900 0.02098300 C 2.51829400 -2.88986100 0.43849900 O 1.83846300 -1.94779200 -0.39986100 C 2.11600200 -0.58457000 -0.11556100 C 1.67886600 -0.22595200 1.32724800 O 1.88579000 1.15948300 1.60161500 C 2.38626600 -1.16810000 2.29873100 O 1.92835200 -0.95207800 3.65160000 C 2.08212200 -2.62138200 1.90890000 O 2.69878900 -3.48547100 2.84285800 O 3.50076700 -0.30614700 -0.26750000 P 4.08155300 1.07160700 -1.04148400 O 3.33425300 2.21688100 -0.39821200 O 4.08585900 0.88102900 -2.53461700 O 5.60347000 1.12083600 -0.44276000 P 7.20145400 0.67758900 -0.61513700 O 8.00259900 1.88440900 -0.16353000 O 7.44772600 -0.69261900 -0.04789200 O 7.38664500 0.52874300 -2.25848800 C 7.13514900 1.64312000 -3.10543700 H -8.26966500 -0.31635400 -3.39010400 H -6.78006800 -0.98703800 -4.10376500 H -4.48538300 -0.30910400 -2.61140900 H -6.33289300 0.22965200 1.10686000 H -11.32321400 -1.72372300 1.47014100 H -12.86820400 -1.39217700 0.60831200 H 3.60317600 -2.73169800 0.35646200 H 1.50353600 -0.00715800 -0.81812800 H 0.59572700 -0.39755400 1.43273200 H 2.49823400 1.54090900 0.93792800 H 3.47079800 -0.99865900 2.25513900 H 2.22355800 -1.75183600 4.11383400 H 0.98103700 -2.74528800 1.94168000 H 2.76974800 -4.32962600 2.27556200 H 7.64201400 2.54165000 -2.72302500 H 6.05720900 1.81090100 -3.20099500 H -8.20296000 -0.38704400 -0.55860600 H -7.81963000 -1.99044200 -3.07541600 H -12.02874700 -0.10800400 1.49068600 H 7.55027300 1.39231100 -4.09348000 H -3.05794800 0.60927200 0.06789400 O -2.19064000 0.91807300 0.41490700 C -3.51988900 2.87999400 0.89678800 C -3.60170300 4.16204800 1.44850500 C -2.48180600 4.75480700 2.03749000 C -1.27566400 4.03972500 2.06005500 C -1.17013000 2.75735300 1.51927400 C -2.30565300 2.16492100 0.93285900 H -4.38470600 2.42287500 0.42972500 H -4.54906500 4.69609900 1.40813800 H -2.54195500 5.75443000 2.46166900 H -0.38746100 4.48515800 2.49876800 H -0.20576800 2.25310400 1.54527300 O 2.61905300 -5.18022100 0.91812000 1 2 1.0 32 1.0 33 1.0 49 1.0 2 3 1.5 4 2.0 3 5 1.5 48 1.0 4 6 1.5 34 1.0 5 6 1.5 35 1.0 6 7 8 1.0 36 1.0 37 1.0 50 1.0 8 9 2.0 10 2.0 9 10 11 12 2.0 12 13 1.0 65 2.0 13 14 1.0 20 1.0 38 1.0 14 15 1.0 15 16 1.0 22 1.0 39 1.0 16 17 1.0 18 1.0 40 1.0 17 41 1.0 18 19 1.0 20 1.0 42 1.0 19 43 1.0 20 21 1.0 44 1.0 21 45 1.0 22 23 1.0 23 24 2.0 25 2.0 26 1.0 24 25 26 27 1.0 27 28 2.0 29 2.0 30 1.0 28 29 30 31 1.0 31 46 1.0 47 1.0 51 1.0 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 1.0 53 59 1.0 54 55 1.5 59 1.5 60 1.0 55 56 1.5 61 1.0 56 57 1.5 62 1.0 57 58 1.5 63 1.0 58 59 1.5 64 1.0 59 60 61 62 63 64 65 |
2楼2012-02-18 19:27:58
muxiachuixue
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不好意思，写错了，这个才是输入文件 %nprocshared=12 %mem=4000MB # opt freq b3lyp/6-31+g(d,p) geom=connectivity initial1_opt+freq_6-31+g(d,p) -4 1 C -1 35.74600000 17.70700000 37.06500000 C 0 34.55400000 17.07300000 36.42100000 N 0 33.71300000 16.21900000 37.09900000 C 0 34.06300000 17.16500000 35.16400000 C 0 32.75500000 15.81100000 36.28600000 N 0 32.94400000 16.37000000 35.10600000 C -1 36.35100000 12.23000000 39.59000000 C 0 35.34500000 12.95400000 38.70400000 O 0 34.80500000 13.99300000 39.14400000 O 0 35.09900000 12.48100000 37.57000000 O 0 30.05008229 18.16819493 37.00040235 C 0 30.19200000 19.39400000 36.80100000 C 0 29.71700000 19.83800000 35.40200000 O 0 30.84500000 19.59000000 34.47800000 C 0 30.55300000 19.94300000 33.07600000 C 0 29.26000000 19.22600000 32.62500000 O 0 29.00000000 19.60800000 31.28500000 C 0 28.05500000 19.60200000 33.54500000 O 0 26.86400000 18.93900000 33.11100000 C 0 28.43700000 19.11400000 34.95000000 O 0 27.39300000 19.41500000 35.90000000 O 0 30.30000000 21.33400000 32.86000000 P 0 31.19300000 22.65600000 33.07400000 O 0 31.44800000 23.34400000 31.81100000 O 0 32.37400000 22.26500000 33.80900000 O 0 30.20000000 23.61800000 33.89000000 P 0 29.91600000 23.94900000 35.42400000 O 0 28.85600000 24.94800000 35.42400000 O 0 29.69100000 22.74800000 36.18500000 O 0 31.22700000 24.58900000 35.96000000 C -1 31.71100000 25.80900000 35.39300000 H 0 36.26137112 16.91621446 37.56893534 H 0 36.23792923 18.25830768 36.29107141 H 0 34.46998508 17.74793333 34.36434265 H 0 31.96071532 15.14099832 36.54116580 H 0 36.86206837 12.99186768 40.14069662 H 0 36.89985044 11.57832409 38.94271205 H 0 29.45011886 20.87410038 35.41505577 H 0 31.42755844 19.65406833 32.53142125 H 0 29.38882618 18.16611236 32.69529934 H 0 29.72891881 20.13942462 30.95657156 H 0 27.86180339 20.65415741 33.52176510 H 0 26.14592876 19.14344770 33.71446900 H 0 28.58582374 18.05513240 34.91061856 H 0 27.75118215 19.95416339 36.60894879 H 0 30.87236139 26.46227634 35.27128188 H 0 32.31703394 25.55346377 34.54900705 H 0 33.83353238 15.88732079 38.03466065 H 0 35.49730535 18.42234640 37.82086407 H 0 35.88600556 11.59973646 40.31900483 H 0 32.35305485 26.24353604 36.13045780 H 0 31.96751104 16.63649352 33.53018581 O 0 31.39310568 16.88254181 32.80140688 C 0 32.60136031 15.06120516 31.78645413 C 0 32.81251344 14.26275187 30.66201733 C 0 32.02421115 14.43705893 29.52473184 C 0 31.02340425 15.40939592 29.51196969 C 0 30.81204569 16.20730021 30.63634211 C 0 31.60132781 16.03347904 31.77354474 H 0 33.22327326 14.92391946 32.68284676 H 0 33.60150888 13.49683836 30.67223884 H 0 32.19100051 13.80817139 28.63817768 H 0 30.40194302 15.54660803 28.61516698 H 0 30.02336623 16.97369697 30.62659861 O 0 30.67728943 20.12328595 37.69270408 1 2 1.0 32 1.0 33 1.0 49 1.0 2 3 1.5 4 2.0 3 5 2.0 48 1.0 4 6 1.5 34 1.0 5 6 2.0 35 1.0 6 7 8 1.0 36 1.0 37 1.0 50 1.0 8 9 2.0 10 2.0 9 10 11 12 1.5 12 13 1.0 65 1.5 13 14 1.0 20 1.0 38 1.0 14 15 1.0 15 16 1.0 22 1.0 39 1.0 16 17 1.0 18 1.0 40 1.0 17 41 1.0 18 19 1.0 20 1.0 42 1.0 19 43 1.0 20 21 1.0 44 1.0 21 45 1.0 22 23 1.0 23 24 2.0 25 2.0 26 1.5 24 25 26 27 1.5 27 28 2.0 29 2.0 30 1.5 28 29 30 31 1.0 31 46 1.0 47 1.0 51 1.0 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 1.0 53 59 1.0 54 55 1.5 59 1.5 60 1.0 55 56 1.5 61 1.0 56 57 1.5 62 1.0 57 58 1.5 63 1.0 58 59 1.5 64 1.0 59 60 61 62 63 64 65 |
3楼2012-02-18 19:30:31
4楼2012-02-18 23:00:45