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amber 加中性化离子遇到问题 已有1人参与
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教程上说 (5)加中性化离子： >addions dna1 Na+ 0 (0意味着中性化) 18 Na+ ions required to neutralize. Adding 18 counter ions to "dna1" using 1A grid Grid extends from solute vdw + 1.87 to 7.97 Resolution: 1.00 Angstrom. grid build: 0 sec (no solvent present) Calculating grid charges charges: 0 sec Placed Na+ in dna1 at (-0.73, 10.83, 18.51). Placed Na+ in dna1 at (6.27, -8.17, 18.51). Placed Na+ in dna1 at (10.27, 4.83, 11.51). Placed Na+ in dna1 at (-6.73, -8.17, 11.51). Placed Na+ in dna1 at (-5.73, 3.83, 13.51). Placed Na+ in dna1 at (-9.73, 3.83, 25.51). Placed Na+ in dna1 at (6.27, -8.17, 5.51). Placed Na+ in dna1 at (-5.73, 8.83, 1.51). Placed Na+ in dna1 at (11.27, 1.83, 25.51). Placed Na+ in dna1 at (-10.73, -4.17, 28.51). Placed Na+ in dna1 at (5.27, 3.83, 3.51). Placed Na+ in dna1 at (2.27, -6.17, 27.51). Placed Na+ in dna1 at (-10.73, -3.17, 8.51). Placed Na+ in dna1 at (6.27, 7.83, 15.51). Placed Na+ in dna1 at (10.27, -3.17, 8.51). Placed Na+ in dna1 at (-1.73, -12.17, 16.51). Placed Na+ in dna1 at (-9.73, 3.83, 4.51). Placed Na+ in dna1 at (-7.73, 8.83, 21.51). Done adding ions. 产生中性化的prmtop和inpcrd文件： 但是我操作后怎么产生的是如下信息： > addions dna1 Na+ 0 18 Na+ ions required to neutralize. Adding 18 counter ions to "dna1" using 1A grid Grid extends from solute vdw + 4.98 to 11.08 Resolution: 1.00 Angstrom. grid build: 0 sec (no solvent present) Calculating grid charges charges: 1 sec Placed Na+ in dna1 at (8.11, -5.38, 12.46). Placed Na+ in dna1 at (7.11, 6.62, 19.46). Placed Na+ in dna1 at (-9.89, 9.62, 12.46). Placed Na+ in dna1 at (-8.89, -10.38, 21.46). Placed Na+ in dna1 at (0.11, 13.62, 8.46). Placed Na+ in dna1 at (-13.89, -1.38, 17.46). Placed Na+ in dna1 at (1.11, -12.38, 12.46). Placed Na+ in dna1 at (-3.89, 9.62, 25.46). Placed Na+ in dna1 at (12.11, 2.62, 14.46). Placed Na+ in dna1 at (-10.89, -5.38, 5.46). Placed Na+ in dna1 at (-11.89, -2.38, 31.46). Placed Na+ in dna1 at (12.11, -9.38, 25.46). Placed Na+ in dna1 at (-8.89, 9.62, -0.54). Placed Na+ in dna1 at (13.11, -7.38, 0.46). Placed Na+ in dna1 at (11.11, 9.62, 6.46). Placed Na+ in dna1 at (3.11, -14.38, 23.46). Placed Na+ in dna1 at (-11.89, 9.62, 21.46). Placed Na+ in dna1 at (15.11, -1.38, 29.46). Done adding ions. 这是什么意思，怎么解决？ |
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感谢参与，应助指数 +1
月只蓝: 金币+1, 鼓励交流 2014-01-17 12:36:02
感谢参与，应助指数 +1
月只蓝: 金币+1, 鼓励交流 2014-01-17 12:36:02
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月只蓝: 金币+1, 鼓励交流 2014-01-18 08:16:14
月只蓝: 金币+1, 鼓励交流 2014-01-18 08:16:14
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4楼2014-01-17 19:18:11
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