Gold Docking- Problem!!!

Question

[Ewelina]

Hello, I have a problem. I don't know, where I made a mistake. I got only a communicate:

Fatal error: get bond type: don't know about bond type Ar

I don't know what it means? Could You help me?

[Vladimir Chupakhin]

It's problem with either protein or ligand file

Answer 1

[Neilfws]

I haven't used the software but apparently, GOLD uses SYBYL bond types as described in this documentation.

One of these types is ar (aromatic), so perhaps one of your files contains instead Ar (upper-case A) and this causes the problem?

There seems to be plenty of documentation which you should read; this type of software is often complex and you can't just jump in and expect it to work.