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

[Amir Zeb]

Hello Tasneem,

Same like you, I'm pretty new to this field too. I don't know enough how to
calculate free energy in gromacs. I did only MM/PBSA for binding energy
calculations.
I'll let you know if i get some thing relevant to your question.

All the best.

Thanks

On Thu, Jan 5, 2017 at 10:28 PM, tasneem kausar 
wrote:

> Dear all
>
> It is first time I am calculating free energy of protein and ligand. I am
> following the Justin's tutorial of methane in water free energy
> calculations. Though only van der waal lambda are defined so I have taken
> the mdp files from the alchemistry.org web page. Since the ligand and
> protein under my study have positive charges (one positive charge on ligand
> and tree positive charges on protein). So I have to add a CL ions in
> topology file to make a neutral sytem.
> Is it okay to use the system with ion for free energy calculation?
> If yes, What are change that can be made in mdp entry.
>
> Waiting for suggestions
> Thanks in Advance
> --
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Re: [gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

Thanks again

That is it what I was asking. I have seen the topology files of t4-lysozyme
with its ligand. It was provided by alchemistry.org tutorial. Can I change
the topology accordingly.
Another thing is the charge on the ligand molecule. How this will be
handled in free energy calculations.

Waiting for your suggestion

On Sat, Jan 7, 2017 at 10:35 AM, Amir Zeb  wrote:

> well
> if you are confident of your simulation you may definitly go ahead with
> this ff
> otherwise you will have to change the ff for simulation too
> i think this is not rational to simulate the system with one ff and then
> change the ff for free energy calculations
>
> good luck
>
> On Jan 7, 2017 2:01 PM, "tasneem kausar" 
> wrote:
>
> > 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 <
> tasneemkausa...@gmail.com
> > >
> > wrote:
> >
> > > mm/pbsa calculates binding energy. I have used that.
> > >
> > > On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb  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" 
> > >> 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
> > >> > --
> > >> > Gromacs Users mailing list
> > >> >
> > >> > * Please search the archive at http://www.gromacs.org/
> > >> > Support/Mailing_Lists/GMX-Users_List before posting!
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> > >> >
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Re: [gmx-users] Free energy calculation of protein and drug

[Amir Zeb]

well
if you are confident of your simulation you may definitly go ahead with
this ff
otherwise you will have to change the ff for simulation too
i think this is not rational to simulate the system with one ff and then
change the ff for free energy calculations

good luck

On Jan 7, 2017 2:01 PM, "tasneem kausar"  wrote:

> 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  >
> wrote:
>
> > mm/pbsa calculates binding energy. I have used that.
> >
> > On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb  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" 
> >> 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
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at http://www.gromacs.org/
> >> > Support/Mailing_Lists/GMX-Users_List before posting!
> >> >
> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
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> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> > send a mail to gmx-users-requ...@gromacs.org.
> >> >
> >> --
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> >>
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> >>
> >
> >
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Re: [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 
wrote:

> mm/pbsa calculates binding energy. I have used that.
>
> On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb  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" 
>> 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
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at http://www.gromacs.org/
>> > Support/Mailing_Lists/GMX-Users_List before posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] Free energy calculation of protein and drug

[Amir Zeb]

alright
why do you care of forcefield in terms of free energy calculations?
do you have literature in reference for your protein simulated with a
specific ff?

On Jan 7, 2017 1:38 PM, "tasneem kausar"  wrote:

> mm/pbsa calculates binding energy. I have used that.
>
> On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb  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" 
> > 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
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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Re: [gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

mm/pbsa calculates binding energy. I have used that.

On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb  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" 
> 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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Free energy calculation of protein and drug

[Amir Zeb]

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"  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
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

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

[tasneem kausar]

Dear all

It is first time I am calculating free energy of protein and ligand. I am
following the Justin's tutorial of methane in water free energy
calculations. Though only van der waal lambda are defined so I have taken
the mdp files from the alchemistry.org web page. Since the ligand and
protein under my study have positive charges (one positive charge on ligand
and tree positive charges on protein). So I have to add a CL ions in
topology file to make a neutral sytem.
Is it okay to use the system with ion for free energy calculation?
If yes, What are change that can be made in mdp entry.

Waiting for suggestions
Thanks in Advance
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