this package is still actively maintained! It will take me a while to get back up to speed, but my needs are the same as they were back then when I published some docking work using the code: I use openbabel to convert pdb files to mol2 adding bond orders and protonation states for ...
楼主求助，我也在纠结这个PDB转成mol2，第一次用openbabel。不会转，网上又找不到教程。真心求助！
我尝试过将其在chemdraw上画出来，保存为cdx格式，再用openbabel转换为mol2格式进行筛选，但系统说我的...
I wonder if anyone can help me work out what's going on here. I'm trying to convert a PDB file of ADP (from structure 3ATV) to mol2 format and add hydrogens. The first step seems to work fine: babel -ipdb 3ATV_ADP.pdb -omol2 3ATV_ADP1.mol2 -p 7.4 however as a check I ...
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Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021),https://doi.org/10.1093/nar/gkab294 dockerbioinformaticspdbprotein-structuresingularitypython-bindingsscientific-computingopenbabelplip ...
然后Pymol file 打开上面的pdb Pymol打开蛋白,点A去掉蛋白的水分子 然后file export molecular pdb 格式 (A clear everything)然后重新打开这个文件 用sele-h-valence 去掉不必要的小分子细节,把hydrogen也隐藏。 找到氢键:A find polar contact , to other atoms in objects....
如何用open babel软件把PDB格式的文件转换成mol2格式 我来答 为你推荐: 特别推荐 如真有龙,它的飞行原理是什么? 古代的夏天有冰镇食品吃吗? 中国首次敲奥运之门,有多艰难? 神农架深处:为何会被列为禁区? 等你来答 换一换 帮助更多人 下载百度知道APP,抢鲜体验 使用百度知道APP,立即抢鲜体验。你...
(e.g., PDB or CIF files), atoms closer than 0.63 Å are not bonded. A further filtering pass is made to ensure standard bond valency is maintained; each element has a maximum number of bonds, if this is exceeded then the longest bonds to an atom are successively removed until the ...
PDB: Read/write PDB insertion codes (Steffen Möller)PNG: Options to crop the margin, and ...