no template found for amino acid

[mrugesh parasa]

Below is the error I get.

error_notemplate.jpg (153.32 KiB) Viewed 182 times

Also attached are the code and the pdb file.

EGFP-E20F20.txt

(1.41 KiB) Downloaded 10 times

https://drive.google.com/file/d/13ycQF0 ... sp=sharing

[Peter Eastman]

There's a discussion of this error message at https://github.com/openmm/openmm/wiki/F ... s#template. Can you take a look and see if the problem is one of the things described there?

[mrugesh parasa]

Sorry, you already told what the error is at this post- viewtopicPhpbb.php?f=161&t=10764&p=0&st ... eaa8dddd43

However, I do not know how to resolve it.

[mrugesh parasa]

I am interested in finding the interaction between two identical proteins.
I duplicated the molecule in pymol and saved the file with two proteins.
How should I duplicate the protein using pymol in a way that openmm understands?

[Peter Eastman]

Just add a line between the end of the first chain and the start of the second one that reads

Code: Select all

TER   

That tells it these are two different chains, so they aren't bonded to each other.

[mrugesh parasa]

Thank you. I included the TER.
I get this new error now.

error_arrayforcebuffer.jpg (115.85 KiB) Viewed 138 times

Here is the code I use.

EGFP-E20F20.txt

(1.41 KiB) Downloaded 12 times

[Peter Eastman]

Well, it's getting a lot further now. That's actually a very unusual error. It's a low level error trying to allocate memory on the GPU. What kind of GPU do you have?