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[求助]
学amber tutorial 遇到参数文件无法产生，急求答案
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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 FATAL: Atom .R FATAL: Atom .R FATAL: Atom .R FATAL: Atom .R FATAL: Atom .R FATAL: Atom .R FATAL: Atom .R FATAL: Atom .R FATAL: Atom .R FATAL: Atom .R FATAL: Atom .R |
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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
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
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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 |
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