[gmx-users] helix change to coil for residues His 177 and His 187 after pdb2gmx in opls-aa forcefield

[Min Wu]

Hello Justin,

Thank you for your reply. But the problem is after even 90ns production
simulation, the random coil of these two spots never change. The right
helix structure never comes back anymore.

Thank you.

Min

On Mon, Sep 17, 2018 at 4:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/17/18 6:42 PM, Min Wu wrote:
>
>> Hi All,
>>
>>
>> When I use pdb2gmx of gromacs 5.0.7 to convert 2lsb.pdb to gro file, the
>> initial helix structure of His 177 and His 187 change to coil. I modified
>> the His to HISD  in the original pdb to match the residue name in opls-aa
>> forcefield.  When I change HISD back to HIS, when viewed in VMD, the helix
>> is back. But when using pdb2gmx, I always got error information, if I keep
>> HIS as the residue name.
>>
>> Do you have any idea what might be the possible problem? Thank you.
>>
>
> VMD is simply guessing the secondary structure wrong. pdb2gmx does not
> change coordinates, but conversion from .pdb to .gro does sacrifice one
> decimal point of precision, which can cause VMD to screw up secondary
> structure rendering. It's functionally meaningless, and since you're going
> to do a simulation anyway, the structure will change somewhat.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
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