[gmx-users] SS bond forcing

[Pierre THEVENET]

In most cases (it is form predicted structures) if the bonds is not formes,
the S atoms are at the opposite side of the backbone. And I work on
peptides, so the length of the structure isn't that big (50 residues max)

--------------------------

Pierre THEVENET
Ph.D. Candidate
INSERM - MTi
Ecole Doctorale B3MI
Université Paris Diderot - Paris 7




2012/4/10 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> Pierre THEVENET wrote:
>
>> How long the MD simulation should be? The problem is that I run multiple
>> simulation (a hundred at a time) and the MD are really time consuming. I
>> should probably can't do it, if the time you propose is too long, I
>> probably forget it.
>>
>>
> I can't predict how much time it would take.  How far apart are the S
> atoms from one another?  If it's just a small distance beyond the normal
> cutoff, it should be quick, a few hundred ps or less (assuming everything
> else is otherwise stable).  If the distance is very long and would require
> large structural transitions to accommodate, then you're probably in
> trouble.
>
> -Justin
>
>  Thank you
>>
>> --------------------------
>>
>> Pierre THEVENET
>> Ph.D. Candidate
>> INSERM - MTi
>> Ecole Doctorale B3MI
>> Université Paris Diderot - Paris 7
>>
>>
>>
>>
>> 2012/4/10 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>
>>
>>
>>
>>    pithevenet at free.fr <mailto:pithevenet at free.fr> wrote:
>>
>>
>>        Here is what I have done:
>>
>>        First, I created the .gro file with the command line:
>>        pdb2gmx  -f test.pdb  -o test.gro  -p test.top -ignh -missing
>>
>>
>>        Then, I added at the end of my test.top file the following lines
>>        (I double checked the atom numbers):
>>
>>        [ distance_restraints ]
>>        ; ai aj type index type' low up1 up2 fac
>>         37 140 1   0     1     0.19 0.21 0.22 1
>>
>>        then, I done:
>>        editconf -f test.gro -o test-box.gro -d 2.0 -c -bt cubic
>>
>>        grompp -c test-box.gro -p test.top -o test-min.tpr -f test-em.mdp
>>
>>        mdrun -s test-min.tpr -c test-min.gro -deffnm test-min -v -nice 0
>>
>>
>>        and finally get my new pdb file with:
>>
>>        editconf -f test-min.gro -o test-min.pdb
>>
>>        But it didn't seemed it had make the two sufur atom closer than
>>        if I didn't add the distance_restrain in the top file.
>>
>>        Did I do something wrong?
>>
>>
>>    Simple energy minimization is unlikely to give rise to the
>>    structural changes you need to bring these atoms close together.
>>     Running a short MD simulation may work, though if the atoms are
>>    very far apart and you force them together quickly, you may have
>>    stability issues.
>>
>>
>>    -Justin
>>
>>    --     ==============================**__==========
>>
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    <tel:%28540%29%20231-9080>
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
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> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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