Charmm力场残基调不出来!!!
各位大侠,帮我看看我建的charmm力场残基哪里错了,怎么总调不出来啊。top文件看着结构正确,但是一到了生成.psf文件,总是看不到甲酰基了。这是为什么呀。RESI FVA 0.00! ?????????????????
GROUP
ATOM H1 HA 0.0900 !
AOTM CN C 0.4200! O1H1
ATOM O1 O -0.5100! \\ /
GROUP ! CN
ATOM N NH1 -0.47 ! | HG11 HG12
ATOM HN H 0.31 !HN-N \ /
ATOM CA CT1 0.07 ! | CG1--HG13
ATOM HA HB 0.09 ! | /
GROUP !HA-CA--CB-HB
ATOM CB CT1 -0.09 ! | \
ATOM HB HA 0.09 ! | CG2--HG21
GROUP ! O=C / \
ATOM CG1CT3 -0.27! | HG21 HG22
ATOM HG11 HA 0.09
ATOM HG12 HA 0.09
ATOM HG13 HA 0.09
GROUP
ATOM CG2CT3 -0.27
ATOM HG21 HA 0.09
ATOM HG22 HA 0.09
ATOM HG23 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CN H1 CN N !ADDED
BOND CBCA CG1 CB CG2 CB N HN
BOND N CA C CA C +N CA HA
BOND CBHB CG1 HG11CG1 HG12CG1 HG13CG2 HG21
BOND CG2 HG22CG2 HG23
DOUBLE O C
DOUBLE O1CN !ADDED
IMPR N CN CA HN C CA +N O !DEVISED
IMPR CN H1 NO1 !ADDED
DONOR HN N
ACCEPTOR O C
ACCEPTOR O1 CN !ADDED 拓扑文件:
CRYST1 1.000 1.000 1.00090.0090.0090.00 P 1 1
ATOM 1C FVA B 1 -3.601-1.112 1.1221.000.00 C
ATOM 2N FVA B 1 -2.790-0.273 3.2891.000.00 N
ATOM 8O1FVA B 1 -1.654-1.703 4.5991.000.00 O
ATOM 9CNFVA B 1 -1.848-0.560 4.1931.000.00 C
ATOM 3O FVA B 1 -4.079-0.123 0.5691.000.00 O
ATOM 4CAFVA B 1 -3.692-1.240 2.6561.000.00 C
ATOM 5CBFVA B 1 -5.139-1.025 3.1621.000.00 C
ATOM 6CG1 FVA B 1 -6.098-2.056 2.5401.000.00 C
ATOM 7CG2 FVA B 1 -5.228-1.135 4.6951.000.00 C
ATOM 10N GLY B 2 -3.016-2.098 0.4231.000.00 N
ATOM 11CAGLY B 2 -2.942-2.115-1.0431.000.00 C
ATOM 12C GLY B 2 -1.745-2.884-1.6261.000.00 C
ATOM 13O GLY B 2 -1.304-3.888-1.0671.000.00 O
ATOM 14N ALA B 3 -1.246-2.424-2.7831.000.00 N
ATOM 15CAALA B 3 -0.164-3.034-3.5601.000.00 C
ATOM 16C ALA B 3 1.183-2.330-3.3061.000.00 C
ATOM 17O ALA B 3 1.354-1.157-3.6411.000.00 O
ATOM 18CBALA B 3 -0.548-3.004-5.0461.000.00 C
ATOM 19N DLE B 4 2.144-3.047-2.7111.000.00 N
ATOM 20CADLE B 4 3.438-2.522-2.2761.000.00 C
ATOM 21CBDLE B 4 4.478-2.618-3.4161.000.00 C
ATOM 22CGDLE B 4 5.381-1.374-3.5361.000.00 C
ATOM 23CD1 DLE B 4 4.620-0.203-4.1791.000.00 C
ATOM 24CD2 DLE B 4 5.986-0.945-2.1891.000.00 C
ATOM 25C DLE B 4 3.891-3.263-1.0031.000.00 C
ATOM 26O DLE B 4 4.172-4.459-1.0501.000.00 O
ATOM 27N ALA B 5 3.926-2.564 0.1361.000.00 N
ATOM 28CAALA B 5 4.073-3.132 1.4761.000.00 C
ATOM 29C ALA B 5 2.865-2.767 2.3621.000.00 C
ATOM 30O ALA B 5 2.395-1.632 2.3331.000.00 O
ATOM 31CBALA B 5 5.390-2.644 2.0911.000.00 C
ATOM 32N DVA B 6 2.375-3.718 3.1681.000.00 N
ATOM 33CADVA B 6 1.274-3.529 4.1251.000.00 C
ATOM 34CBDVA B 6 1.856-3.304 5.5421.000.00 C
ATOM 35CG1 DVA B 6 2.750-2.051 5.5911.000.00 C
ATOM 36CG2 DVA B 6 0.763-3.150 6.6121.000.00 C
ATOM 37C DVA B 6 0.312-4.734 4.0671.000.00 C
ATOM 38O DVA B 6 0.758-5.880 4.0791.000.00 O
ATOM 39N VAL B 7 -1.003-4.481 4.0021.000.00 N
ATOM 40CAVAL B 7 -2.063-5.494 3.8851.000.00 C
ATOM 41C VAL B 7 -2.643-5.475 2.4541.000.00 C
ATOM 42O VAL B 7 -3.205-4.465 2.0351.000.00 O
ATOM 43CBVAL B 7 -3.161-5.243 4.9481.000.00 C
ATOM 44CG1 VAL B 7 -4.120-6.441 5.0331.000.00 C
ATOM 45CG2 VAL B 7 -2.585-4.994 6.3531.000.00 C
ATOM 46N DVA B 8 -2.512-6.569 1.6901.000.00 N
ATOM 47CADVA B 8 -2.916-6.643 0.2761.000.00 C
ATOM 48CBDVA B 8 -4.346-7.217 0.1171.000.00 C
ATOM 49CG1 DVA B 8 -5.407-6.406 0.8781.000.00 C
ATOM 50CG2 DVA B 8 -4.762-7.249-1.3661.000.00 C
ATOM 51C DVA B 8 -1.898-7.471-0.5291.000.00 C
ATOM 52O DVA B 8 -1.895-8.699-0.4431.000.00 O
ATOM 53N TRP B 9 -1.073-6.811-1.3531.000.00 N
ATOM 54CATRP B 9 -0.197-7.450-2.3391.000.00 C
ATOM 55C TRP B 9 1.255-6.938-2.2571.000.00 C
ATOM 56O TRP B 9 1.487-5.756-2.0101.000.00 O
ATOM 57CBTRP B 9 -0.791-7.242-3.7421.000.00 C
ATOM 58CGTRP B 9 -0.016-7.880-4.8571.000.00 C
ATOM 59CD1 TRP B 9 -0.148-9.158-5.2791.000.00 C
ATOM 60CD2 TRP B 9 1.064-7.306-5.6521.000.00 C
ATOM 61NE1 TRP B 9 0.751-9.413-6.2961.000.00 N
ATOM 62CE2 TRP B 9 1.534-8.307-6.5601.000.00 C
ATOM 63CE3 TRP B 9 1.715-6.047-5.6831.000.00 C
ATOM 64CZ2 TRP B 9 2.587-8.067-7.4621.000.00 C
ATOM 65CZ3 TRP B 9 2.769-5.793-6.5881.000.00 C
ATOM 66CH2 TRP B 9 3.205-6.800-7.4761.000.00 C
ATOM 67N DLE B10 2.229-7.826-2.5041.000.00 N
ATOM 68CADLE B10 3.663-7.527-2.5481.000.00 C
ATOM 69CBDLE B10 4.281-8.165-3.8091.000.00 C
ATOM 70CGDLE B10 5.766-7.815-4.0391.000.00 C
ATOM 71CD1 DLE B10 6.288-8.599-5.2531.000.00 C
ATOM 72CD2 DLE B10 5.975-6.312-4.2731.000.00 C
ATOM 73C DLE B10 4.346-8.006-1.2551.000.00 C
ATOM 74O DLE B10 4.864-9.122-1.1951.000.00 O
ATOM 75N TRP B11 4.349-7.156-0.2211.000.00 N
ATOM 76CATRP B11 5.026-7.388 1.0581.000.00 C
ATOM 77C TRP B11 4.122-7.105 2.2731.000.00 C
ATOM 78O TRP B11 3.146-6.360 2.1941.000.00 O
ATOM 79CBTRP B11 6.314-6.545 1.1021.000.00 C
ATOM 80CGTRP B11 7.316-6.842 0.0221.000.00 C
ATOM 81CD1 TRP B11 7.891-8.046-0.1991.000.00 C
ATOM 82CD2 TRP B11 7.839-5.957-1.0171.000.00 C
ATOM 83NE1 TRP B11 8.739-7.977-1.2851.000.00 N
ATOM 84CE2 TRP B11 8.747-6.710-1.8291.000.00 C
ATOM 85CE3 TRP B11 7.644-4.596-1.3621.000.00 C
ATOM 86CZ2 TRP B11 9.430-6.143-2.9211.000.00 C
ATOM 87CZ3 TRP B11 8.325-4.015-2.4561.000.00 C
ATOM 88CH2 TRP B11 9.218-4.785-3.2321.000.00 C
ATOM 89N DLE B12 4.478-7.699 3.4181.000.00 N
ATOM 90CADLE B12 3.815-7.517 4.7101.000.00 C
ATOM 91CBDLE B12 4.891-7.387 5.8071.000.00 C
ATOM 92CGDLE B12 5.923-6.264 5.5551.000.00 C
ATOM 93CD1 DLE B12 5.269-4.886 5.3741.000.00 C
ATOM 94CD2 DLE B12 6.918-6.212 6.7241.000.00 C
ATOM 95C DLE B12 2.823-8.668 4.9741.000.00 C
ATOM 96O DLE B12 3.159-9.643 5.6461.000.00 O
ATOM 97N TRP B13 1.599-8.549 4.4401.000.00 N
ATOM 98CATRP B13 0.484-9.481 4.6471.000.00 C
ATOM 99C TRP B13 -0.432-9.576 3.4091.000.00 C
ATOM 100O TRP B13 -0.697-8.579 2.7391.000.00 O
ATOM 101CBTRP B13 -0.322-9.048 5.8871.000.00 C
ATOM 102CGTRP B13 0.417-9.111 7.1941.000.00 C
ATOM 103CD1 TRP B13 0.522 -10.204 7.9831.000.00 C
ATOM 104CD2 TRP B13 1.218-8.075 7.8431.000.00 C
ATOM 105NE1 TRP B13 1.316-9.925 9.0771.000.00 N
ATOM 106CE2 TRP B13 1.783-8.628 9.0361.000.00 C
ATOM 107CE3 TRP B13 1.543-6.729 7.5391.000.00 C
ATOM 108CZ2 TRP B13 2.623-7.884 9.8861.000.00 C
ATOM 109CZ3 TRP B13 2.386-5.973 8.3841.000.00 C
ATOM 110CH2 TRP B13 2.925-6.548 9.5541.000.00 C
ATOM 111N DLE B14 -0.942 -10.785 3.1321.000.00 N
ATOM 112CADLE B14 -1.907 -11.086 2.0701.000.00 C
ATOM 113CBDLE B14 -3.152 -11.759 2.6841.000.00 C
ATOM 114CGDLE B14 -3.880 -10.920 3.7551.000.00 C
ATOM 115CD1 DLE B14 -4.374-9.572 3.2071.000.00 C
ATOM 116CD2 DLE B14 -5.074 -11.718 4.2991.000.00 C
ATOM 117C DLE B14 -1.270 -11.976 0.9821.000.00 C
ATOM 118O DLE B14 -1.190 -13.193 1.1501.000.00 O
ATOM 119N TRP B15 -0.840 -11.379-0.1391.000.00 N
ATOM 120CATRP B15 -0.378 -12.088-1.3421.000.00 C
ATOM 121C TRP B15 0.834 -11.412-2.0201.000.00 C
ATOM 122O TRP B15 1.325 -10.375-1.5771.000.00 O
ATOM 123CBTRP B15 -1.569 -12.235-2.3111.000.00 C
ATOM 124CGTRP B15 -2.763 -12.957-1.7511.000.00 C
ATOM 125CD1 TRP B15 -2.881 -14.299-1.6281.000.00 C
ATOM 126CD2 TRP B15 -3.969 -12.397-1.1481.000.00 C
ATOM 127NE1 TRP B15 -4.075 -14.616-1.0111.000.00 N
ATOM 128CE2 TRP B15 -4.783 -13.478-0.6831.000.00 C
ATOM 129CE3 TRP B15 -4.456 -11.083-0.9311.000.00 C
ATOM 130CZ2 TRP B15 -6.017 -13.269-0.0391.000.00 C
ATOM 131CZ3 TRP B15 -5.698 -10.861-0.2951.000.00 C
ATOM 132CH2 TRP B15 -6.475 -11.950 0.1551.000.00 C
ATOM 133CAETA B16 2.416 -11.475-3.9191.000.00 C
ATOM 134N ETA B16 1.320 -12.008-3.1161.000.00 N
ATOM 135CBETA B16 2.559 -12.262-5.2271.000.00 C
ATOM 136O ETA B16 3.528 -11.647-6.0511.000.00 O
END 只要帮我看看Charmm力场残基的甲酰胺部分(CN O1 H1)和我加了标注的地方有没有问题就可以啦,别的地方是从缬氨酸拷过来的,应该不会有问题的。谢谢啦! 终于找到问题的所在了,各位看官请注意:top文件的第四行本来应该是“ATOM”,写成了“AOTM”;就这么小的一个错误,让我忙活了好几天。真是千里长堤,溃于蚁穴,教训深刻呀!!!
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