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RUBi-ZA / MD-TASK

Tool suite for analysing molecular dynamics trajectories using network analysis and PRS
GNU General Public License v3.0
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PRS input files ???? #52

Closed Vasudha-pai closed 4 months ago

Vasudha-pai commented 5 months ago

Hello, I've found the MDM task tool very useful, however I had a query regarding the input files. In the mdm-task-web> mdmtaskweb_tutorial.ipynb the --final file was taken from the Protein data bank. however, in the MD task manual, it says to use the final pdb file of the target conformation. Can I please have clarity on what should be the input files while working with MDM task. is it a pdb file from the protein data bank or final md topology pdb file?

oliserand commented 5 months ago

Hi Vasudha,

Thanks for using MDM-TASK-web. The target conformation in PRS is one that is homologous to the starting structure, but has a different conformation. The two conformations need to have the same number of CA atoms. One basically wants to know if you nudge each residue of a starting conformation, how likely is the nudged protein resembling a certain target conformation, assuming an underlying linear model of motion. It builds that model from an equilibrated portion of an MD trajectory. In the end, you end up finding potential allosteric sites. You could read up more about it here: https://pubs.acs.org/doi/10.1021/acs.jcim.6b00775#

Kind regards, Olivier

On Wed, Apr 17, 2024 at 11:27 AM Vasudha-pai @.***> wrote:

Hello, I've found the MDM task tool very useful, however I had a query regarding the input files. In the mdm-task-web> mdmtaskweb_tutorial.ipynb the --final file was taken from the Protein data bank. however, in the MD task manual, it says to use the final pdb file of the target conformation. Can I please have clarity on what should be the input files while working with MDM task. is it a pdb file from the protein data bank or final md topology pdb file?

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Vasudha-pai commented 5 months ago

Thank you so much for your response Oliver. I took the first frame as my initial conformation and the last frame from the trajectory file as my final conformation. but I keep getting an error saying that the trajectory and topology files do not have the same number of atoms. but when I take the entire frames as my initial conformation I get the graph. So I was genuinely confused if I was doing it right. Thanks again!

oliserand commented 5 months ago

No problem. My best guess is that you might not have the same number of atoms in your trajectory and the coordinate/topology file.

On Thu, 18 Apr 2024 at 12:11, Vasudha-pai @.***> wrote:

Thank you so much for your response Oliver. I took the first frame as my initial conformation and the last frame from the trajectory file as my final conformation. but I keep getting an error saying that the trajectory and topology files do not have the same number of atoms. but when I take the entire frames as my initial conformation I get the graph. So I was genuinely confused if I was doing it right. Thanks again!

— Reply to this email directly, view it on GitHub https://github.com/RUBi-ZA/MD-TASK/issues/52#issuecomment-2063511087, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB6K6CEBSXVHNKYXV5NOR3LY56L37AVCNFSM6AAAAABGK5VXMCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRTGUYTCMBYG4 . You are receiving this because you commented.Message ID: @.***>