[gmx-users] analyzing docking + MD results

[MD]

Hi Mark,
I looked through the page and links. Is the "Free energy calculations" of
tutorial 6 the one you recommended for binding energy analysis?
Thanks,
Ming

On Sun, Dec 24, 2017 at 7:08 AM, MD <refmac5 at gmail.com> wrote:

> Excellent. Thank you Mark.
> Happy holidays.
> Ming
>
> On Dec 23, 2017 10:14 PM, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>
>> Hi,
>>
>> Yes, GROMACS will do that. See
>> http://www.alchemistry.org/wiki/Example_Free_Energy_Calculations (and
>> many
>> other resources)
>>
>> Mark
>>
>> On Sun, Dec 24, 2017 at 10:29 AM MD <refmac5 at gmail.com> wrote:
>>
>> > Hi Mark,
>> >
>> > Does GROMACS do that or I need to go with other software?
>> >
>> > Thank you,
>> >
>> > Ming
>> >
>> > On Dec 23, 2017 6:06 PM, "Mark Abraham" <mark.j.abraham at gmail.com>
>> wrote:
>> >
>> > > Hi,
>> > >
>> > > Normally one would try to compute the relative free energy of binding
>> > > between the two poses, but that is rather more costly than what you've
>> > done
>> > > so far.
>> > >
>> > > Mark
>> > >
>> > > On Sun, Dec 24, 2017, 07:24 MD <refmac5 at gmail.com> wrote:
>> > >
>> > > > Hi Gromacs folks,
>> > > >
>> > > > I want to look at protein peptide interaction. After docking two
>> > > > conformations of the peptide emerged, and both of which make
>> chemistry
>> > > > sense and have similar low binding energies. (+-1 kj/mol). The
>> distance
>> > > > between the two conformations of the peptide is ~8A.
>> > > >
>> > > > Then I tried simulations on the two scenarios of protein peptide
>> > > complexes
>> > > > and the results showed the peptide only shifted very slightly in
>> both
>> > > > simulations. The rmsd, and energy dropping are all similar. I
>> wonder if
>> > > > there are other ways to make a judgement to tell which conformation
>> of
>> > > the
>> > > > peptide makes more sense by analyzing their MD results?
>> > > >
>> > > > Thanks,
>> > > >
>> > > > Ming
>> > > > --
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