[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 suggestions. I will have a try.

Min

On Mon, Sep 17, 2018 at 4:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/17/18 6:57 PM, Min Wu wrote:
>
>> 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.
>>
>
> Are you basing this assessment solely on what you see with VMD? Again, it
> is very sensitive and can be wrong. Use a real analysis method like DSSP.
>
> -Justin
>
>
> 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
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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