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benniu2004

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[ÇóÖú] amber ½Ì³Ì3.5ÖУ¬ÎÞ·¨Éú³É¸´ºÏÌåµÄ²ÎÊýÎļþ ÒÑÓÐ1È˲ÎÓë

ÔÚamberµÄ½Ì³Ì3.5ÖУ¬http://ambermd.org/tutorials/adv ... script/section5.htm£¬ ÏÂÔØÁ˸´ºÏÌåµÄpdbÎļþEstrogen_Receptor-Raloxifene.pdb£¬È»ºó²ð³öµ°°×ºÍС·Ö×ÓÁ½¸ö²¿·Ö¡£ÔÚÉú³É.inpcrdʱ£¬µ°°×ºÍС·Ö×ÓÁ½²¿·Ö¶¼Ã»ÓÐÎÊÌ⣬µ«ÊÇÔÚÉú³É¸´ºÏÌåµÄ²ÎÊýÎļþʱ×ÜÊDZ¨´í£º
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.
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ÎÒÓõÄtleapÊäÈëÎļþÊÇ£º
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
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