rpestana94 发表于 2022-5-7 23:24
So right now all is working without any problem right

是的是的 非常感谢老师指点

DSF 发表于 2022-5-6 21:25
更新一下最新进展，我改了一下min的输入文件，之前因为看教程一直是用的ntc=2 ntf=2，我当时看到说这是tip3 ...

So right now all is working without any problem right

更新一下最新进展，我改了一下min的输入文件，之前因为看教程一直是用的ntc=2 ntf=2，我当时看到说这是tip3p的一个三点水模型应该用的参数，所以我一直用的这个，之前跑的体系可能是因为pdb很好，因为教程也是用的一个好的pdb，但不是所有pdb都是好的，例如我现在跑的这个，优化的第一步需要使用ntc=1 ntf=1 允许键的收缩变化，这样那些有问题的键就可以得到优化了，现在min也正常了。有类似报错的小伙伴可以排查一下这一点。

rpestana94 发表于 2022-5-6 23:14
you give a dimer, I was just asking because sometimes we don't need to work with the dimer, hope y ...

目前试了一下还是不行，我是不是步骤出了问题。我是把去掉小分子的蛋白用pdb4amber处理去水加H，然后对小分子reduce加H，使用antechamber和parmchk2生成了mol2和frcmod文件，tleap导入小分子生成lig。然后我就把加了H的小分子加到对pdb4amber处理后的蛋白pdb中，生成complex结构，然后tleap，但是还是有类似之前的错误出现。求老师分享一下老师处理的流程呢？我感觉我的流程可能本身就是不对的。

DSF 发表于 2022-5-6 09:43
老师，我蛋白本身确实是二聚体，不过我已经取了单体出来准备就模拟这个，我给的pdb结构就是单体的呀？非 ...

you give a dimer, I was just asking because sometimes we don't need to work with the dimer, hope you can solve your problem if not let me know

rpestana94 发表于 2022-5-6 22:10
It looks good, there are a few residues which look weird, like the TYR612, also you have a protein ...

老师，我蛋白本身确实是二聚体，不过我已经取了单体出来准备就模拟这个，我给的pdb结构就是单体的呀？非常感谢老师的提议，我之前是使用H++ server去准备蛋白文件的，我这次试一下，按照您说的步骤进行，看看能不能解决。非常非常感谢！

DSF 发表于 2022-5-6 07:48
其中original是初始结构另外一个是我tleap之后的结构

It looks good, there are a few residues which look weird, like the TYR612, also you have a protein dimer, do you need to work with the dimer? maybe you can work with just one chain.

I try with the original file and didn't get any error, try erasing all hydrogen and water molecules from the original file, try using pdb4amber to prepare the file (it's already installed with ambertools), erase waters from the original.

其中original是初始结构另外一个是我tleap之后的结构

rpestana94 发表于 2022-5-6 20:21
Can you upload your structure?, at the beginning it looks like it is something weird with the struct ...

好的好的，我马上发一下，谢谢老师回复

Can you upload your structure?, at the beginning it looks like it is something weird with the structure, maybe the protein structure or the small molecules