[gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

Thanks Amir Zeb for your reply
I have read in literature about the FEPsetup to parametrize the complex
file (protein+drug) for simulation. This setup builds files based on amber.
Since I have previously used 54a7ff to simulate the protein and drug and
topology files were generated from ATB in gromos54a7 format. Since I didn't
find free energy calculation of protein and ligand with this force field.
Thats why I was confused to proceed further using the same.

On Sat, Jan 7, 2017 at 10:07 AM, tasneem kausar <tasneemkausar12 at gmail.com>
wrote:

> mm/pbsa calculates binding energy. I have used that.
>
> On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb <zebamir85 at gmail.com> wrote:
>
>> hello
>> you may use mm/pbsa compiled with gromacs to calculate free energy
>> all the best
>>
>> On Jan 7, 2017 1:27 PM, "tasneem kausar" <tasneemkausar12 at gmail.com>
>> wrote:
>>
>> > Dear gromacs users
>> >
>> > It is first time I am trying to perform free energy calculation of
>> protein
>> > and drug complex. I am following Justin' s tutorial of mehtane in water.
>> > That calculation are performed on a neutral system. If the ligand
>> molecule
>> > has charge what are the provisions that could be taken into account.
>> > I have performed my MD simulation using force field gromos54a7. And Now
>> I
>> > am trying to go onward using free energy calculations. Since the free
>> > energy calculations are performed on ambed99ldn, opls and charmm force
>> > fields (as I know from the articles). Is it okay to use gromos54a7 ff
>> for
>> > free energy calculations.
>> >
>> > Kindly tell me
>> >
>> > Thanks in Advance
>> > --
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