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专业: 理论和计算化学

[求助] amber 加中性化离子遇的到问题已有2人参与

做amber官网的第一个练习
加中性化离子时，应该是这样：
(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：
>saveamberparm dnal ployAT_cio prmtop ployAT_cio.inpcrd
输出：polyAT_cio.prmtop,  polyAT_cio.inpcrd
最终的目的是建立带有抗性离子的可溶的DNA文件，抗性已建立，接下来创建可溶性的文件，也就是加水。

我输入
>saveamberparm dnal ployAT_cio prmtop ployAT_cio.inpcrd

后，产生如下问题：
> saveamberparm dnal ployAT_cio prmtop ployAT_cio.inpcrd
saveAmberParm: Improper number of arguments!
usage:  saveAmberParm <unit> <topologyfile> <coordfile>
>
而且没有输出 polyAT_cio.prmtop,  polyAT_cio.inpcrd 文件
这是为什么？

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