aanma with rtb=TRUE still distorts residues

[Former user]

I'm running aanma and setting rtb to TRUE in order to prevent intra-residue distortion. However, regardless of whether I set rtb to TRUE or FALSE, many residues are very badly distorted with their bonds become extremely long. I've tried various setting to nmer, but this only seems to limit the overall flexibility of the molecule.

[Robert DeLisle]

Sorry about the anonymous issue. I failed to login when I posted. This comment should have my correct user id

[Xinqiu Yao]

Hi,

Were you looking at the interpolated trajectory generated from a mode vector using mktrj()? I think it is normal if residues are distorted, especially when the amplitude is set too large, because normal mode analysis assumes harmonic potential, which is only valid near the energy minimum for any real protein system. And this is true no matter setting rtb or not.

You may try to do a few steps of energy minimization for each frame generated by mktrj(). This will give you a more "realistic" trajectory.

[Robert DeLisle]

Does Bio3d provide minimization? I didn't see that as an optionoption. If it doesn't, what can I use for protein minimization? GROMACS is the only thing that comes to mind, but that's a heavy dependency for a quick minimization.

[Xinqiu Yao]

No, Bio3D doesn't do energy minimization. You need MD software such as Gromacs or Amber...

[Xinqiu Yao]

Not a bug.

[Barry Grant]

Not a bug