Search found 20 matches

by mrugesh parasa
Mon Sep 16, 2019 11:51 am
Forum: OpenMM
Topic: no template found for amino acid
Replies: 6
Views: 187

Re: no template found for amino acid

Thank you. I included the TER.
I get this new error now.
error_arrayforcebuffer.jpg
error_arrayforcebuffer.jpg (115.85 KiB) Viewed 143 times
Here is the code I use.
EGFP-E20F20.txt
(1.41 KiB) Downloaded 17 times
by mrugesh parasa
Sun Sep 15, 2019 5:47 pm
Forum: OpenMM
Topic: no template found for amino acid
Replies: 6
Views: 187

Re: no template found for amino acid

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?
by mrugesh parasa
Sun Sep 15, 2019 5:40 pm
Forum: OpenMM
Topic: no template found for amino acid
Replies: 6
Views: 187

Re: no template found for amino acid

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.
by mrugesh parasa
Sun Sep 15, 2019 5:00 pm
Forum: OpenMM
Topic: no template found for amino acid
Replies: 6
Views: 187

no template found for amino acid

Below is the error I get.
error_notemplate.jpg
error_notemplate.jpg (153.32 KiB) Viewed 187 times
Also attached are the code and the pdb file.
EGFP-E20F20.txt
(1.41 KiB) Downloaded 16 times
https://drive.google.com/file/d/13ycQF0 ... sp=sharing
by mrugesh parasa
Fri Sep 13, 2019 8:28 am
Forum: OpenMM
Topic: pdb file does not open in openmm
Replies: 14
Views: 469

Re: pdb file does not open in openmm

Has the fixed version been released?
by mrugesh parasa
Thu Sep 05, 2019 3:54 pm
Forum: OpenMM
Topic: pdb file does not open in openmm
Replies: 14
Views: 469

Re: pdb file does not open in openmm

Below is the error I get.
openmm-error.jpg
openmm-error.jpg (558 KiB) Viewed 176 times
by mrugesh parasa
Sat Aug 31, 2019 3:07 pm
Forum: OpenMM
Topic: pdb file does not open in openmm
Replies: 14
Views: 469

Re: pdb file does not open in openmm

I get the following error.
openmm_error.jpg
openmm_error.jpg (74.71 KiB) Viewed 178 times
by mrugesh parasa
Wed Aug 28, 2019 4:25 pm
Forum: OpenMM
Topic: pdb file does not open in openmm
Replies: 14
Views: 469

Re: pdb file does not open in openmm

This attached file opened a month back with openmm-setup. Now it is not opening. Not sure why.
EGFP-E20F20_2molecules.rar
(199.25 KiB) Downloaded 13 times
by mrugesh parasa
Tue Aug 27, 2019 5:14 pm
Forum: OpenMM
Topic: pdb file does not open in openmm
Replies: 14
Views: 469

Re: pdb file does not open in openmm

I converted the attached file to pdb format (I saved it from pymol as a pdb file). This is still not opening with openmm-setup
EGFP-E20F20_pdb.rar
(99.96 KiB) Downloaded 15 times
by mrugesh parasa
Tue Aug 27, 2019 4:56 am
Forum: OpenMM
Topic: pdb file does not open in openmm
Replies: 14
Views: 469

Re: pdb file does not open in openmm

Can't openmm be changed to accept this format?