normal Side chain fix (scFix)

  • LJefferys
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7 years 11 months ago #5535 by LJefferys
Side chain fix (scFix) was created by LJefferys
Hi,

I am trying to modify my protein model to incorporate the side chain fixes implemented in the recent JCTC paper from Herzog et al. but have had no success with the tcl script provided. Might anyone please be able to help me understand how to implement the changes? All I get from the tcl script is the output on the console:

load pdb file 1FGY
moving CA and CB to center of mass of BB, SC1 bead
ERROR: did not recognize residue MSE
ERROR: did not recognize residue MSE
measuring SC BB BB SC dihedrals
[ dihedrals ]
; SC-BB-BB-SC dihedrals
[ angles ]
; SC-BB-BB and BB-BB-SC

Any advice would be really appreciated. Or, if you have some other way of implementing the changes, please could you advise me as to this?

Best wishes,
Lizzie

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7 years 10 months ago - 7 years 10 months ago #5555 by Florian
Replied by Florian on topic Side chain fix (scFix)
Hi Lizzie,

Thanks for trying to implement the scFix modification.

The script doesn't recognize the amino acid MSE. Would it make sense to change it to MET? You can modify your atomistic structure and load it in VMD and apply the script on that structure. Just delete the following line from the script, while keeping your atomistic structure as 'top':

> mol new $pdbcode

I hope that helps.

Cheers,
Florian
Last edit: 7 years 10 months ago by Florian.

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7 years 10 months ago #5561 by LJefferys
Replied by LJefferys on topic Side chain fix (scFix)
Hi Florian,

Thank you very much for your reply. That seems to have worked - thank you for your help!

Best wishes,
Lizzie

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7 years 10 months ago #5562 by flaviyan
Replied by flaviyan on topic Side chain fix (scFix)
Hi Florian,

Just a quick question here, since you would know better, I noticed that the side chain dihedrals are represented using the restricted dihedral functions (type 10 ) implemented in the Gromacs, may I ask why not use the regular dihedral potential ?

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7 years 10 months ago #5563 by Florian
Replied by Florian on topic Side chain fix (scFix)
Hi Flaviyan,

For the dihedrals, we used the standard dihedral potential in gromacs. However, using only these potentials, the simulations are not stable with a 20fs time step. That's why we had to add the restricted bending potentials for the corresponding side chain (sc) - backbone (bb) - sc and bb-bb-sc angles. These potentials avoid the angles that make the dihedrals unstable.

For more details, check out the following paper:

Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations
Monica Bulacu, Nicolae Goga, Wei Zhao, Giulia Rossi, Luca Monticelli, Xavier Periole, D. Peter Tieleman, and Siewert J. Marrink
Journal of Chemical Theory and Computation 2013 9 (8), 3282-3292
DOI: 10.1021/ct400219n


Best, Florian

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7 years 10 months ago #5565 by flaviyan
Replied by flaviyan on topic Side chain fix (scFix)
Hi Florian,

Thanks for clarifying I thought the dihedrals were "type 10"
I read through the script before running it and got confused with

set n_reb 10

so anyways

The SC-BB-BB-SC dihedral is type 1 with a K = 25 kJ/mol and multiplicity 1

and the SC-BB-SC and BB-BB-SC are type 10 with K = 5 kJ/mol and theta = 100

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