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【求助】做NAMD的1K4C.pdb時候出現(xiàn)的錯誤
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你可以把所有的輸入寫道一個tc腳本中, 比如名字為11.tcl 然后在11.tcl中寫入: mol delete all mol load pdb KCSA-ALL.pdb foreach S { A B C D } { set seg [atomselect top "segname $S and chain C and protein"] $seg writepdb seg$S.pdb $seg delete } 然后在vmd的 Extensions → Tk Console 中直接source 11.tcl即可 當(dāng)然了,首先你要確保在KCSA-ALL.pdb文件的目錄下面,否則找不到pdb,也是白搭,或者你可以告訴KCSA-ALL.pdb的路徑,總之,要確保KCSA-ALL.pdb能被找到 我建議你先把我給你的11.tcl復(fù)制,看行不行,因為你的錯誤確實很像你自己的疏忽所致,呵呵 |
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使用source buildpsf.tcl的時候,出現(xiàn)錯誤: reading topology file ../top_all27_prot_lipid.rtf > CHARMM22 All-Hydrogen Topology File for Proteins and Lipids << >>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<< >>>>>>>>>>>>>>>>>>>>>> July 2004 <<<<<<<<<<<<<<<<<<<<<<<<<< All comments to ADM jr. via the CHARMM web site: www.charmm.org parameter set discussion forum Created by CHARMM version 31 1 cross-term entries present in topology definitions aliasing residue HIS to HSE aliasing residue ILE atom CD1 to CD aliasing residue HOH atom O to OH2 aliasing residue HOH to TIP3 building segment A reading residues from pdb file segA.pdb unknown residue type K unknown residue type K unknown residue type K unknown residue type K unknown residue type K unknown residue type K unknown residue type K unknown residue type DGA extracted 169 residues from pdb file Info: generating structure... unknown residue type K ERROR: failed on end of segment MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over. |
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