你好，我的好像和你的类似，缺少结晶水的角度参数，请问该如何解决呢？
/opt/amber22/bin/teLeap: Error!
Could not find angle parameter for atom types: HW - Y4 - HW
        for atom H1 at position 8.762411, -11.683037, -11.870854,
            atom O at position 7.805411, -11.683037, -11.870854,
        and atom H2 at position 7.565411, -10.756037, -11.870854.

/opt/amber22/bin/teLeap: Error!
Could not find angle parameter for atom types: HW - Y5 - HW
        for atom H1 at position 10.797411, -9.612037, -12.714854,
            atom O at position 9.840411, -9.612037, -12.714854,
        and atom H2 at position 9.600411, -8.685037, -12.714854.

/opt/amber22/bin/teLeap: Error!
Could not find angle parameter for atom types: HW - Y6 - HW
        for atom H1 at position 8.124411, -8.884037, -11.312854,
            atom O at position 7.167411, -8.884037, -11.312854,
        and atom H2 at position 6.927411, -7.957037, -11.312854.
Building proper torsion parameters.
Building improper torsion parameters.
total 2760 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.

/opt/amber22/bin/teLeap: Warning!
Parameter file was not saved.

kongmenghua 发表于 2024-5-11 17:56
你好，这个问题解决了嘛，我也出现了这样的问题

非标准氨基酸的两端不要只用氢原子补全，用ACE和NME封端后再进行参数生成，就不会有参数缺少的问题了。

你好，这个问题解决了嘛，我也出现了这样的问题

ovolcano 发表于 2023-10-23 16:39
我的非标准氨基酸残基主链应该是NT-CT-C（NT是与上一个残基的C相连的原子，CT是αC原子，C是与下一个残基 ...

直接写 source leaprc.protein.ff19SB 就可以了，19SB的参数里面有C-N*。用其他的AMBER力场也可以，根据实际的需求决定。

八月的雨季 发表于 2023-10-22 15:25
就是你漏掉了一些键、角参数，补上就行了

是需要自己手动补上吗？

Frozen-Penguin 发表于 2023-10-21 20:54
C-NT这个键应该是肽键里面的吧，所以不会出现在残基内，如果你是按照antechamber的流程做的，过程中应该 ...

我的非标准氨基酸残基主链应该是NT-CT-C（NT是与上一个残基的C相连的原子，CT是αC原子，C是与下一个残基的N相连的原子），C和NT没有相连，要说C-NT键存在那应该是非标准残基与相邻残基形成的键，那我生成的非标准残基的参数确实是没有这个键的参数的。关于您说的这个“肽键的参数之间用amber力场的”应该怎么做？

就是你漏掉了一些键、角参数，补上就行了

ovolcano 发表于 2023-10-21 03:42
The parameter information of the angle that was not found also should not exist in my protein. Bec ...

Sometimes the error is due to the name of the residue but usually when you load the prep and frcmod file that you create this error is solve

ovolcano 发表于 2023-10-21 09:52
这个是我生成的prepin文件，从文件看C和NT应该没有成键，所以我觉得生成的frcmod文件应该没有缺少信息， ...

C-NT这个键应该是肽键里面的吧，所以不会出现在残基内，如果你是按照antechamber的流程做的，过程中应该写过一个主链信息文件，这个文件里写了这个键的信息。如果非标准残基的参数用了gaff2，肽键的参数之间用amber力场的就可以了。

rpestana94 发表于 2023-10-21 10:54
Which is the non-standard residue and what about the angle parameters which are the other giving you ...

The parameter information of the angle that was not found also should not exist in my protein. Because there is no C-NT bond in the protein, there should naturally be no information about the angles formed by C, NT  and other atoms. And after checking, the BOND section in the obtained frcmod file includes all the bonds of the non-standard residue. I don't see any problems with the preprin and frcmod files. I want to know why it still looks for information about this C-NT bond which should not already exist?

Which is the non-standard residue and what about the angle parameters which are the other giving you errors

What you show is just the parameters for bond and C-T bond dosen't exist, you should create the parameters for this residue and the problem will be solve, this can be done using gaussian to calculate the charges and obtain the prepi and frcmod file