Hello,

I'm working with a metalloenzyme that has a catalytic Zinc center. I want to incorporate the Zinc atom vdw parameters into the Tripos52_vdw.prm file, but I don't understand what the K value means. I'm assuming that the R value is the vdw radius of the atom and I was going to use a 1.200 value for the Zinc atom; as the rest of the metals in the file. I'm searching for references to acquire those values because I understand that Zinc has variable coordination. Can you please help me with this issue?

Many thanks,

Islam K. Matar

Brilliant!

Thanks a million for all your time and effort.

All the best.

@alchemistcai

Many thanks @alchemistcai I really appreciate your help.

I modified the RbtIonicAtoms.prm, Tripos52_vdw.prm, and Tripos52_vdw.prm.old files (please find attached).

I still get the following warning when I run rbcavity or rbdock:

RbtMOL2FileSource: INFO Attempting to identify element by 1st 2 chars of FFType string: Zn

RbtMOL2FileSource: INFO Atomic number = 30

RbtMOL2FileSource: WARNING Undefined Tripos type for UNK:ZN_262:ZN

Is the software just giving me a heads-up? Or should I do something to stop that warning?

Thanks again,

Islam

Tripos52_vdw.prm.old

RbtIonicAtoms.prm

Tripos52_vdw.prm

Hello,

I'm working with a metalloenzyme that has a catalytic Zinc center. I want to incorporate the Zinc atom vdw parameters into the Tripos52_vdw.prm file, but I don't understand what the K value means. I'm assuming that the R value is the vdw radius of the atom and I was going to use a 1.200 value for the Zinc atom; as the rest of the metals in the file. I'm searching for references to acquire those values because I understand that Zinc has variable coordination. Can you please help me with this issue?

Many thanks,

Islam K. Matar