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

[Justin Lemkul]

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

==================================================