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panhuairen金虫 (小有名气)
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[交流]
【求助】Amber 的Xleap 遇到的问题
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为了把InsightII 产生的RNA的pdb文件进行分子模拟，就将该文件到xleap下进行跑动力学之前的准备，以便生成计算前的文件格式： Here are commands: ________________________________________________________________________ >[root@localhost amber_tutorial]# $AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.rna.ff99 -I: Adding /usr/local/amber9/dat/leap/prep to search path. -I: Adding /usr/local/amber9/dat/leap/lib to search path. -I: Adding /usr/local/amber9/dat/leap/parm to search path. -I: Adding /usr/local/amber9/dat/leap/cmd to search path. -s: Ignoring startup file: leaprc -f: Source /usr/local/amber9/dat/leap/cmd/leaprc.rna.ff99. Welcome to LEaP! Sourcing: /usr/local/amber9/dat/leap/cmd/leaprc.rna.ff99 Log file: ./leap.log Loading parameters: /usr/local/amber9/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 Loading library: /usr/local/amber9/dat/leap/lib/all_nucleic94.lib Loading library: /usr/local/amber9/dat/leap/lib/all_amino94.lib Loading library: /usr/local/amber9/dat/leap/lib/all_aminoct94.lib Loading library: /usr/local/amber9/dat/leap/lib/all_aminont94.lib Loading library: /usr/local/amber9/dat/leap/lib/ions94.lib Loading library: /usr/local/amber9/dat/leap/lib/solvents.lib > x = loadpdb "final_bf_dm.pdb" Loading PDB file: ./final_bf_dm.pdb Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: H2* within residue: .R Created a new atom named: HO2* within residue: .R ................................ ............. ....... Created a new atom named: HO2* within residue: .R Created a new atom named: H2* within residue: .R Created a new atom named: HO2* within residue: .R Created a new atom named: H2* within residue: .R Created a new atom named: HO2* within residue: .R Created a new atom named: H2* within residue: .R Created a new atom named: HO2* within residue: .R Created a new atom named: H2* within residue: .R Created a new atom named: HO2* within residue: .R total atoms in file: 1944 Leap added 194 missing atoms according to residue templates: 70 Heavy 124 H / lone pairs The file contained 195 atoms not in residue templates > ___________________________________________________________________ 谁知道问题出在哪里了呢？ [ Last edited by zzgyb on 2008-7-20 at 18:59 ] |
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