Gromacs配体问题
Hi, everyone:>> I am a new user of Gromacs, and I am running through the tutorial.
>> When I am trying to run the ligand-receptor binding tutorial from
>>
>> http://www.bevanlab.biochem.vt.e ... ex/02_topology.html
>> I met some trouble in adding ion.
>> Each time when I use genion, it shows:
>>
>> Will try to add 0 NA ions and 6 CL ions.
>> Select a continuous group of solvent molecules
>> Group 0 ( System) has 33046 elements
>> Group 1 ( Protein) has1693 elements
>> Group 2 ( Protein-H) has1301 elements
>> Group 3 ( C-alpha) has 163 elements
>> Group 4 ( Backbone) has 489 elements
>> Group 5 ( MainChain) has 653 elements
>> Group 6 ( MainChain+Cb) has 805 elements
>> Group 7 ( MainChain+H) has 815 elements
>> Group 8 ( SideChain) has 878 elements
>> Group 9 ( SideChain-H) has 648 elements
>> Group 10 ( Prot-Masses) has1693 elements
>> Group 11 ( non-Protein) has 31353 elements
>> Group 12 ( Other) has 15 elements
>> Group 13 ( JZ4) has 15 elements
>> Group 14 ( Water) has 31338 elements
>> Group 15 ( SOL) has 31338 elements
>> Group 16 ( non-Water) has1708 elements
>> Select a group: 15
>> Selected 15: 'SOL'
>> Number of (3-atomic) solvent molecules: 10446
>>
>> Processing topology
>>
>> Back Off! I just backed up temp.top to ./#temp.top.3#
>>
>> -------------------------------------------------------
>> Program genion_d, VERSION 4.5.4
>> Source code file: gmx_genion.c, line: 285
>>
>> Fatal error:
>>No line with moleculetype 'SOL' found the [ molecules ] section of file
>> 'topol.top'
who can tell me the reason?ge wei gaoshou bang bang mang ba! 好像说的很清楚了，top文件里没有溶剂，你在按着教程重新来一遍吧。。。 在top文件中添加上电荷，阳离子NA，阴离子CL，注意添加了后要减去相应溶剂数，要改top文件，或者直接用-p XXX.top M命令添加也行。 我想我知道是什么原因了，应该是top文件中SOL那一行没有单独出来，如图，只要回车下一行就可以啦 dmarkfree 发表于 2013-10-31 10:06
我想我知道是什么原因了，应该是top文件中SOL那一行没有单独出来，如图，只要回车下一行就可以啦 ...
你好，我回车到下一行也没有用啊
还有别的解决方法吗
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