求助：使用H++计算蛋白质的PKa值时出现报错

wyxlfw

各位老师好，我想模拟在不同的pH下，蛋白质与小分子的结合情况。在论坛里面发现老师有给出可以用H++预测蛋白质的质子化情况，但是我导入pdb文件以后，却出现了错误。
错误信息如下：
The information retrieved from your structure:

cwd:/home/shared_utilities/completion/frontend/uploads/Wuyuxin/3aup popen:Resource id #5 Title: 3aup.pdb: unknown
pH: unknown
Model Count: 1
ESTIMATED RUN TIME: 0 hrs 22 min 8 sec (Actual time will vary depending on load on the H++ server)
THE CALCULATION HAS STOPPED. It appears that some residues are missing in the middle of the uploaded structure. When residues are missing (that is the sequence in the PDB file is discontigous) the accuracy of pK estimates of any kind is affected, especially in the vicinity of the gaps. Make sure there are no "gaps" in your structure, see the FAQ for suggestions. It is also possible that your structure contains non-standard residue names, sometimes listed as HETATM, in the main sequence. These will not be recognized by the system and will be treated as missing, resulting in the above error. Please change the names to comply with the standard amino-acid nominclature. Alternatively, you can supply your own PQR file -- the naming complience is not enforced then. See the FAQ. The following error message may help you identify the location of the error in the PDB/PQR input file
FAILURE: Sequence discontinuity occured between residues 123 and 128 at the line ATOM 905 N LEU A 128 -4.401 -54.332 -10.728 1.00 63.20 N
想请问我该如何解决这个问题呢？希望得到老师们的回复。

Serious

1）你的输入命令是什么呢？
2）看你报错信息是蛋白结构不完整，补全之后就好了吧？（H++没用过）；

wyxlfw

Serious 发表于 2023-10-15 11:15
1）你的输入命令是什么呢？
2）看你报错信息是蛋白结构不完整，补全之后就好了吧？（H++没用过）；

您好老师。
1.我是将蛋白质的PDB文件上传然后就出现报错。
2.我现在这个问题已经解决了，但是我使用-inter手动选择质子化的时候，gromacs就开始出现这样的命令：LINK GYS-65 SG-942 and CYS-79 SG-1128（y/n）？是什么情况呢？

Serious

wyxlfw 发表于 2023-10-15 22:11
您好老师。
1.我是将蛋白质的PDB文件上传然后就出现报错。
2.我现在这个问题已经解决了，但是我使用-in ...

1）我不是GROMACS的使用者，我猜原因是二硫键，有的程序是会自动判断，你看看结构这两个残基的距离；