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倩430

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[求助] 学amber tutorial 遇到参数文件无法产生，急求答案

在学习amber tutorial 中例子时，按步骤操作给adna加完电荷后出现大量下列错误信息，这是什么原因呀

> addions adna Na+ 0
20 Na+ ions required to neutralize.
Adding 20 counter ions to "adna" using 1A grid
Used default radius  1.50 for 120 atoms
Grid extends from solute vdw + 5.15  to  11.25
Resolution:    1.00 Angstrom.
grid build: 0 sec
(no solvent present)
Calculating grid charges
charges: 1 sec
Placed Na+ in adna at (-4.02, -4.03, -0.36).
Placed Na+ in adna at (-1.02, 3.97, 25.64).
Placed Na+ in adna at (10.98, -11.03, 11.64).
Placed Na+ in adna at (10.98, 7.97, 18.64).
Placed Na+ in adna at (-3.02, -13.03, 3.64).
Placed Na+ in adna at (-5.02, 2.97, -6.36).
Placed Na+ in adna at (14.98, -4.03, 13.64).
Placed Na+ in adna at (-9.02, 8.97, 26.64).
Placed Na+ in adna at (-11.02, 8.97, 10.64).
Placed Na+ in adna at (-10.02, -3.03, 32.64).
Placed Na+ in adna at (3.98, 9.97, 22.64).
Placed Na+ in adna at (2.98, -15.03, 8.64).
Placed Na+ in adna at (2.98, 13.97, 5.64).
Placed Na+ in adna at (-13.02, -6.03, 15.64).
Placed Na+ in adna at (-1.02, 11.97, -9.36).
Placed Na+ in adna at (-14.02, -2.03, -0.36).
Placed Na+ in adna at (13.98, 3.97, 1.64).
Placed Na+ in adna at (-3.02, -14.03, 20.64).
Placed Na+ in adna at (14.98, 2.97, 14.64).
Placed Na+ in adna at (-0.02, -3.03, 31.64).
> saveamberparm adna a-dna_charges_only.prmtop a-dna_charges_only.inpcrd
Checking Unit.
FATAL:  Atom .R.A does not have a type.
FATAL:  Atom .R.A does not have a type.
FATAL:  Atom .R.A does not have a type.
FATAL:  Atom .R.A does not have a type.
FATAL:  Atom .R.A does not have a type.
FATAL:  Atom .R.A does not have a type.
FATAL:  Atom .R.A does not have a type.
FATAL:  Atom .R.A does not have a type.
FATAL:  Atom .R.A does not have a type.
FATAL:  Atom .R.A does not have a type.
FATAL:  Atom .R.A does not have a type.
FATAL:  Atom .R.A does not have a type

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【答案】应助回帖

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感谢参与，应助指数 +1
chaizhm: 金币+3, 很有道理~ 2012-09-26 09:27:33
倩430: 金币+5 2012-09-26 15:03:22

不懂amber
但是这个问题应该比较明了吧，应该是你的输入文件中与参数中的原子类型不对。

这种简单的错误，推荐你google一下，就应该能找到解决的办法，比在这里等待要有效的多。
google “Atom does not have a type amber”

https://www.google.com.hk/search ... =utf-8&oe=UTF-8