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benniu2004

新虫 (小有名气)

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虫号: 1420882
注册: 2011-09-28
专业: 生物大分子结构与功能

[求助] amber 教程3.5中，无法生成复合体的参数文件已有1人参与

在amber的教程3.5中，http://ambermd.org/tutorials/adv ... script/section5.htm，下载了复合体的pdb文件Estrogen_Receptor-Raloxifene.pdb，然后拆出蛋白和小分子两个部分。在生成.inpcrd时，蛋白和小分子两部分都没有问题，但是在生成复合体的参数文件时总是报错：
FATAL:  Atom .R<RAL 241>.A<O16 19> does not have a type.
FATAL:  Atom .R<RAL 241>.A<C17 20> does not have a type.
FATAL:  Atom .R<RAL 241>.A<C22 21> does not have a type.
FATAL:  Atom .R<RAL 241>.A<C21 22> does not have a type.
FATAL:  Atom .R<RAL 241>.A<C18 23> does not have a type.
FATAL:  Atom .R<RAL 241>.A<C19 24> does not have a type.
FATAL:  Atom .R<RAL 241>.A<C20 25> does not have a type.
FATAL:  Atom .R<RAL 241>.A<O23 26> does not have a type.
FATAL:  Atom .R<RAL 241>.A<C24 27> does not have a type.
FATAL:  Atom .R<RAL 241>.A<C25 28> does not have a type.
FATAL:  Atom .R<RAL 241>.A<N26 29> does not have a type.
FATAL:  Atom .R<RAL 241>.A<C27 30> does not have a type.
FATAL:  Atom .R<RAL 241>.A<C28 31> does not have a type.
FATAL:  Atom .R<RAL 241>.A<C29 32> does not have a type.
FATAL:  Atom .R<RAL 241>.A<C30 33> does not have a type.
FATAL:  Atom .R<RAL 241>.A<C31 34> does not have a type.
FATAL:  Atom .R<RAL 241>.A<H1 35> does not have a type.
FATAL:  Atom .R<RAL 241>.A<H2 36> does not have a type.
有没有知道问题原因的虫友？望不吝赐教

我用的tleap输入文件是：
source /root/amber14/dat/leap/cmd/oldff/leaprc.ff99SB
source leaprc.gaff
com = loadpdb Estrogen_Receptor-Ral.pdb
pro = loadpdb receptor.pdb
RAL = loadmol2 RAL.mol2
loadamberparams RAL.frcmod

set default PBRadii mbondi2
saveamberparm com complex.prmtop complex.inpcrd
saveamberparm pro receptor.prmtop receptor.inpcrd
saveamberparm RAL ligand.prmtop ligand.inpcrd
charge com
addions com Na+ 7

solvatebox com TIP3PBOX 12.0
saveamberparm com complex_solvated.prmtop complex_solvated.inpcrd
quit
多谢了！

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