| 查看: 2525 | 回复: 3 | ||
[求助]
新手关于autodock准备ligand分子时出现的问题 已有1人参与
|
|
我是在window xp系统上装的ADT，在准备ligand配体分子时，open分子时弹出一下页面： （请教是什么问题，怎么解决？） Python 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)] on win32 Type "copyright", "credits" or "license()" for more information. **************************************************************** Personal firewall software may warn about the connection IDLE makes to its subprocess using this computer's internal loopback interface. This connection is not visible on any external interface and no data is sent to or received from the Internet. **************************************************************** IDLE 1.2.2 ==== No Subprocess ==== >>> 02: :CYS1:HT2 and 02: :CYS1:HT3 have the same coordinates ERROR ********************************************* Traceback (most recent call last): File "C:\Python25\Lib\site-packages\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto result = command( *args, **kw ) File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1008, in doit initLPO4(mol, cleanup=cleanup) File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4 root=root, outputfilename=outputfilename, cleanup=cleanup) File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1019, in __init__ detect_bonds_between_cycles=detect_bonds_between_cycles) File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 768, in __init__ delete_single_nonstd_residues=False) File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 143, in __init__ self.addCharges(mol, charges_to_add) File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 229, in addCharges chargeCalculator.addCharges(mol.allAtoms) File "C:\Python25\Lib\site-packages\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges babel.assignHybridization(atoms) File "C:\Python25\Lib\site-packages\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization self.valence_two() File "C:\Python25\Lib\site-packages\lib\site-packages\PyBabel\atomTypes.py", line 266, in valence_two angle1 = bond_angle(k.coords, a.coords, l.coords) File "C:\Python25\Lib\site-packages\lib\site-packages\PyBabel\util.py", line 47, in bond_angle raise ZeroDivisionError("Input used:", a, b, c) ZeroDivisionError: ('Input used:', [-11.763, 0.56000000000000005, -0.13400000000000001], [-11.365, 1.5389999999999999, -0.16600000000000001], [-11.365, 1.5389999999999999, -0.16600000000000001]) 02: :CYS1:HT2 and 02: :CYS1:HT3 have the same coordinates ERROR ********************************************* Traceback (most recent call last): File "C:\Python25\Lib\site-packages\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto result = command( *args, **kw ) File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1008, in doit initLPO4(mol, cleanup=cleanup) File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4 root=root, outputfilename=outputfilename, cleanup=cleanup) File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1019, in __init__ detect_bonds_between_cycles=detect_bonds_between_cycles) File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 768, in __init__ delete_single_nonstd_residues=False) File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 143, in __init__ self.addCharges(mol, charges_to_add) File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 229, in addCharges chargeCalculator.addCharges(mol.allAtoms) File "C:\Python25\Lib\site-packages\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges babel.assignHybridization(atoms) File "C:\Python25\Lib\site-packages\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization self.valence_two() File "C:\Python25\Lib\site-packages\lib\site-packages\PyBabel\atomTypes.py", line 266, in valence_two angle1 = bond_angle(k.coords, a.coords, l.coords) File "C:\Python25\Lib\site-packages\lib\site-packages\PyBabel\util.py", line 47, in bond_angle raise ZeroDivisionError("Input used:", a, b, c) ZeroDivisionError: ('Input used:', [-11.763, 0.56000000000000005, -0.13400000000000001], [-11.365, 1.5389999999999999, -0.16600000000000001], [-11.365, 1.5389999999999999, -0.16600000000000001]) |
回复此楼» 猜你喜欢
建议基金发布提前给出明确的时间点
已经有14人回复
-
范进中举一文的中心思想
已经有5人回复
-
2026国自然函评费到账
已经有17人回复
-
让我中一个面上吧！
已经有15人回复
-
2026年的国家社科基金项目通讯评审的新规则与新动向、新挑战
已经有5人回复
-
跳槽后在研项目怎么办？
已经有10人回复
-
什么时候开奖？
已经有10人回复
-
今天放榜吗？
已经有16人回复
-
93BebMhtakh前后11位开头都是大写
已经有8人回复
-
只有每年这种时候来逛逛小木虫
已经有26人回复
» 本主题相关商家推荐: (我也要在这里推广)
» 本主题相关价值贴推荐，对您同样有帮助:
- 怎样使用DS或者是autodock在模拟好的蛋白中加入铜离子
已经有3人回复
- Autodock蛋白处理时，保留在蛋白的原配体如何处理？
已经有12人回复
- 在autodock软件中如何将配体和受体拆分开
已经有9人回复
- 最近在研究autodock.....怎能弄都搞不出来，求大神看看什么原因
已经有21人回复
- 请问准备小分子配体时，有的准备不成功，是什么原因？
已经有5人回复
- pymol 小分子的叠合
已经有15人回复
- 分子对接时配体跟受体分开很远，配体不在受体活性口袋
已经有7人回复
- 分子对接的评价问题
已经有4人回复
- 新手autodock中autogrid出现问题
已经有8人回复
- 关于用DS做虚拟筛选的问题
已经有4人回复
- surflex-dock对接问题
已经有3人回复
- 使用autodock4.2处理分子对接问题，在run autogrid时总是出错，请各位高人指点啊？？
已经有10人回复
- Autodock时 gridbox的参数怎么设置??
已经有18人回复
- autodock安装好后导入分子为什么不对（附图）
已经有18人回复
- 【求助】求助：怎样将Autodock做出来的对接图保存成pdb格式？谢谢
已经有12人回复
- 【求助】如何实现两个小分子之间的对接？！
已经有15人回复
- 【在线答疑】UCSF DOCK分子对接和虚拟筛选
已经有42人回复
- 【原创】AutoDock使用笔记总结－原创始发
已经有32人回复
lynch627
金虫 (小有名气)
- 应助: 1 (幼儿园)
- 金币: 2273.9
- 帖子: 90
- 在线: 45.1小时
- 虫号: 1436292
- 注册: 2011-10-11
- 性别: GG
- 专业: 生物技术药物
2楼2014-06-29 11:28:57
3楼2014-06-29 20:49:19
4楼2014-06-30 21:10:37
40