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no template found for amino acid
Posted: Sun Sep 15, 2019 5:00 pm
by mrugesh
Below is the error I get.
- error_notemplate.jpg (153.32 KiB) Viewed 186 times
Also attached are the code and the pdb file.
https://drive.google.com/file/d/13ycQF0 ... sp=sharing
Re: no template found for amino acid
Posted: Sun Sep 15, 2019 5:20 pm
by peastman
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?
Re: no template found for amino acid
Posted: Sun Sep 15, 2019 5:40 pm
by mrugesh
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.
Re: no template found for amino acid
Posted: Sun Sep 15, 2019 5:47 pm
by mrugesh
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?
Re: no template found for amino acid
Posted: Sun Sep 15, 2019 6:47 pm
by peastman
Just add a line between the end of the first chain and the start of the second one that reads
That tells it these are two different chains, so they aren't bonded to each other.
Re: no template found for amino acid
Posted: Mon Sep 16, 2019 11:51 am
by mrugesh
Thank you. I included the TER.
I get this new error now.
- error_arrayforcebuffer.jpg (115.85 KiB) Viewed 142 times
Here is the code I use.
Re: no template found for amino acid
Posted: Tue Sep 17, 2019 12:54 pm
by peastman
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?