Re: [gmx-users] Binding Free energy calculation

[Dallas Warren]

http://www.alchemistry.org/wiki/Example_Free_Energy_Calculations

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.
On Sun, 25 Nov 2018 at 19:19, KRISHNA PRASAD GHANTA
 wrote:
>
> Dear
>   Gromacs User , I am working on protein and Ionic liquid interaction. I am 
> trying to calculate the Ionic liquid binding free energy per ionic liquid 
> molecule, is there any way by which I can predict the binding free energy
> In pre processing or post processing simulation.
>
>
> --
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[gmx-users] Binding Free energy calculation

[KRISHNA PRASAD GHANTA]

Dear 
  Gromacs User , I am working on protein and Ionic liquid interaction. I am 
trying to calculate the Ionic liquid binding free energy per ionic liquid 
molecule, is there any way by which I can predict the binding free energy 
In pre processing or post processing simulation.


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[gmx-users] Binding free energy calculation

[KRISHNA PRASAD GHANTA]

Dear gmx user 
   I am working on protein ionic liquid interaction. I am trying to calculate 
the binding free energy of ionic liquid (system contain ~ 100 ionic liquid 
molecule). Is there any way to calculate the binding free energy in pre 
processing stage of post processing stage. 
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Re: [gmx-users] binding free energy with gromacs2016

[Justin Lemkul]

On 11/8/16 11:00 AM, Qasim Pars wrote:

Dear users,

Hope someone will answer the questions in my previous mail.

Thanks in advance,


On 6 Nov 2016, at 23:48, Qasim Pars  wrote:

Dear users,

I will try to do binding free energy calculation using GROMACS2016 but I am 
confused a little bit about the preparation of  the input files. I have a few 
questions:

1) There are below lines to apply a harmonic distance restraint in the mdp 
files of the binding free energy tutorial 
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme

pull   = umbrella
pull_geometry  = distance
pull_dim   = Y Y Y
pull_start = no
pull_init1 = 0.654
pull_ngroups   = 1
pull_group0= a_1391
pull_group1= a_2615
pull_k1= 0.0   ; kJ*mol^(-1)*nm^(-2)
pull_kB1   = 4184  ; kJ*mol^(-1)*nm^(-2)

Question 1: Instead of those lines I would like to use the [ 
intermolecular_interactions ] section in the topology file with GROMACS2016. 
Could you please tell me what to write the [ intermolecular_interactions ] 
section?



Why?  The pull code is modulated in a lambda-dependent fashion, which is 
probably part of the tutorial and computed free energy.



2) complex.top file of the tutorial is as follows:
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"

[ atomtypes ]
;name  bond_type  masscharge  ptype   sigma  epsilon
c3c3  0.  0.  A   3.39967e-01  4.57730e-01
dc3   c3  0.  0.  A   0.0e+00  0.0e+00


Question 2: Why all values (sigma and epsilon) of dc3 are zero?



This is effectively a dummy atom, used in transforming the ligand.


[ nonbond_params ]
; i  jfunc  sigma   epsilon
c3   c31 3.3996700e-01   4.5773000e-01
dc3  dc3   1 3.3996700e-01   4.5773000e-01

Question 3: Why all values of dc3 aren't zero?



These are pair-specific interactions.


[ angle_restraints ]
; ai ajakaltype thA  kA multA  thB  kB  
   multB
 1393   1391   2615  1391  188.8 0.00   1  88.8 
41.84   1
 1391   2615   2614  2615  132.9 0.00   1  32.9 
41.84   1

[ dihedral_restraints ]
; aiajakal   type   phiA dphiA   kA  phiB dphiB 
  kB
  1410  1393  1391  2615 1  -159.7  0.0  0.00-159.7   0.0   
  41.84
  1393  1391  2615  2614 1  122.6   0.0  0.00 122.6   0.0   
  41.84
  1391  2615  2614  2610 1  12.80.0  0.00  12.8   0.0   
  41.84
.
Question 4: Do I still need to put those ligand parameters (dc3, [ 
angle_restraints ], [ dihedral_restraints ] ... ) into the topology file to use 
with GROMACS2016?



There is no version-dependent difference here with respect to the topology.

-Justin


I read section 5.4.2 and 6.1 of the GROMACS2016 manual but I couldn't 
understand how to prepare the input files.
--
Qasim Pars


--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] binding free energy with gromacs2016

[Qasim Pars]

Dear users,

Hope someone will answer the questions in my previous mail.

Thanks in advance,

> On 6 Nov 2016, at 23:48, Qasim Pars  wrote:
> 
> Dear users,
> 
> I will try to do binding free energy calculation using GROMACS2016 but I am 
> confused a little bit about the preparation of  the input files. I have a few 
> questions:
> 
> 1) There are below lines to apply a harmonic distance restraint in the mdp 
> files of the binding free energy tutorial 
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
> 
> pull   = umbrella 
> pull_geometry  = distance
> pull_dim   = Y Y Y
> pull_start = no
> pull_init1 = 0.654
> pull_ngroups   = 1
> pull_group0= a_1391
> pull_group1= a_2615
> pull_k1= 0.0   ; kJ*mol^(-1)*nm^(-2)
> pull_kB1   = 4184  ; kJ*mol^(-1)*nm^(-2)
> 
> Question 1: Instead of those lines I would like to use the [ 
> intermolecular_interactions ] section in the topology file with GROMACS2016. 
> Could you please tell me what to write the [ intermolecular_interactions ] 
> section? 
> 
> 2) complex.top file of the tutorial is as follows:
> ; Include forcefield parameters
> #include "amber99sb-ildn.ff/forcefield.itp"
> 
> [ atomtypes ]
> ;name  bond_type  masscharge  ptype   sigma  epsilon
> c3c3  0.  0.  A   3.39967e-01  4.57730e-01
> dc3   c3  0.  0.  A   0.0e+00  0.0e+00
> 
> 
> Question 2: Why all values (sigma and epsilon) of dc3 are zero? 
> 
> [ nonbond_params ]
> ; i  jfunc  sigma   epsilon
> c3   c31 3.3996700e-01   4.5773000e-01
> dc3  dc3   1 3.3996700e-01   4.5773000e-01
> 
> Question 3: Why all values of dc3 aren't zero? 
> 
> [ angle_restraints ]
> ; ai ajakaltype thA  kA multA  thB  
> kB multB
>  1393   1391   2615  1391  188.8 0.00   1  88.8 
> 41.84   1  
>  1391   2615   2614  2615  132.9 0.00   1  32.9 
> 41.84   1 
> 
> [ dihedral_restraints ]
> ; aiajakal   type   phiA dphiA   kA  phiB 
> dphiB   kB
>   1410  1393  1391  2615 1  -159.7  0.0  0.00-159.7   0.0 
> 41.84
>   1393  1391  2615  2614 1  122.6   0.0  0.00 122.6   0.0 
> 41.84
>   1391  2615  2614  2610 1  12.80.0  0.00  12.8   0.0 
> 41.84
> .
> Question 4: Do I still need to put those ligand parameters (dc3, [ 
> angle_restraints ], [ dihedral_restraints ] ... ) into the topology file to 
> use with GROMACS2016?
> 
> I read section 5.4.2 and 6.1 of the GROMACS2016 manual but I couldn't 
> understand how to prepare the input files.
> -- 
> Qasim Pars
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[gmx-users] binding free energy with gromacs2016

[Qasim Pars]

Dear users,

I will try to do binding free energy calculation using GROMACS2016 but I am
confused a little bit about the preparation of  the input files. I have a
few questions:

1) There are below lines to apply a harmonic distance restraint in the mdp
files of the binding free energy tutorial
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme

pull   = umbrella
pull_geometry  = distance
pull_dim   = Y Y Y
pull_start = no
pull_init1 = 0.654
pull_ngroups   = 1
pull_group0= a_1391
pull_group1= a_2615
pull_k1= 0.0   ; kJ*mol^(-1)*nm^(-2)
pull_kB1   = 4184  ; kJ*mol^(-1)*nm^(-2)

Question 1: Instead of those lines I would like to use the [
intermolecular_interactions ] section in the topology file with
GROMACS2016. Could you please tell me what to write the [
intermolecular_interactions ] section?

2) complex.top file of the tutorial is as follows:
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"

[ atomtypes ]
;name  bond_type  masscharge  ptype   sigma  epsilon
c3c3  0.  0.  A   3.39967e-01  4.57730e-01
dc3   c3  0.  0.  A   0.0e+00  0.0e+00


Question 2: Why all values (sigma and epsilon) of dc3 are zero?

[ nonbond_params ]
; i  jfunc  sigma   epsilon
c3   c31 3.3996700e-01   4.5773000e-01
dc3  dc3   1 3.3996700e-01   4.5773000e-01

Question 3: Why all values of dc3 aren't zero?

[ angle_restraints ]
; ai ajakaltype thA  kA multA  thB
 kB multB
 1393   1391   2615  1391  188.8 0.00   1  88.8
41.84   1
 1391   2615   2614  2615  132.9 0.00   1  32.9
41.84   1

[ dihedral_restraints ]
; aiajakal   type   phiA dphiA   kA  phiB
dphiB   kB
  1410  1393  1391  2615 1  -159.7  0.0  0.00-159.7
0.0 41.84
  1393  1391  2615  2614 1  122.6   0.0  0.00 122.6
0.0 41.84
  1391  2615  2614  2610 1  12.80.0  0.00  12.8
0.0 41.84
.
Question 4: Do I still need to put those ligand parameters (dc3, [
angle_restraints ], [ dihedral_restraints ] ... ) into the topology file to
use with GROMACS2016?

I read section 5.4.2 and 6.1 of the GROMACS2016 manual but I couldn't
understand how to prepare the input files.
-- 
Qasim Pars
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Re: [gmx-users] binding free energy

[Billy Williams-Noonan]

Hi Justin,

The free ligand is the ligand in a box of solvent, and the complex is the
complex in a box of solvent.  The complex would need to exist for the
duration of each of your lambda windows for this method to be reliable, and
the system would need to be in equilibrium as well...  Have you considered
steered MD?

I would imagine that you will need pull code constraints holding your amino
acid in place as the VDW and coulomb lambdas get close to 1.  However if
you are performing a relative FEP calculation, you can probably avoid using
restraints depending on whether State B still interacts with the ionic
surface.

You also may or may not find that you will need more coulomb lambdas
depending on how long each window is being simulated for.

You don't need a temperature lambda setting as you are not perturbing the
temperature, I don't think?  Mass lambdas are unnecessary because you
should not be perturbing the mass either in an absolute FEP run.  They are
still unnecessary in a relative run since the mass contributions should
cancel in a closed thermodynamic cycle.  If you are perturbing dihedral
angles though, maybe consider using the FEP-lambdas setting.

Hope you've been going well! :)

Also, this would be my approach.  I know absolute and relative FEP methods
work well for ligands binding to proteins, but I have no experience with
the exact situation that you're describing.

Good luck!

Billy

On 5 July 2016 at 19:09, Alexander Alexander 
wrote:

> Hello Billy,
>
> Thanks for your response.
>
> Please confirm me that with bonded(complex), you mean the geometry of
> "amino acid+solidsurface+ water" that I should harvest in advance by normal
> MD simulation in which amino acid has been absorbed into the surface. and
> then this geometry should be used as the initial structure for each lambda
> in order to do FEP.
>
> Also, what do you mean please by the free (unbound)? If it is a geometry of
> again "amino acid+solidsurface+ water" in which amino acid has been
> solvated in water far away from the solid surface? or just an amino acid
> solvated in a box of water without solid surface (amino acid + water).
>
> Good to know that this strategy is the one mentioned in below paper (Figure
> 1):
> http://pubs.acs.org/doi/full/10.1021/ct400487e
>
> Here is the free energy parameter I am using in my calculation would you
> please comment on it, or let me know if I should consider any other
> parameter changes like mass-restrain-tempetatre-lambda?
>
> free-energy  = yes
> init-lambda-state = MYLAMBDA   ;;;from (i=0;i<15;i++)
> calc-lambda-neighbors= -1
> vdw-lambdas   = 0.00 0.00 0.00 0.00 0.00 0.10 0.20 0.30 0.40
> 0.50 0.60 0.70 0.80 0.90 1.00
> coul-lambdas   = 0.00 0.25 0.50 0.75 1.00 1.00 1.00 1.00 1.00
> 1.00 1.00 1.00 1.00 1.00 1.00
> couple-moltype= Protein_chain_A
> couple-lambda0  = vdw-q
> couple-lambda1  = none
> couple-intramol   = no
> nstdhdl  = 50
> sc-alpha= 0.5
> sc-coul   = no
> sc-power= 1
> sc-sigma= 0.3
>
>
> Thanks.
> Regards,
> Alex
>
>
>
>
> On Tue, Jul 5, 2016 at 3:03 AM, Billy Williams-Noonan <
> billy.williams-noo...@monash.edu> wrote:
>
> > Just to clarify, the formula should be:
> >
> >dG (bind)  = dG (complex) - dG (solv)
> >
> > Billy
> >
> > On Tuesday, 5 July 2016, Billy Williams-Noonan <
> > billy.williams-noo...@monash.edu> wrote:
> >
> > > You would want to perturb your amino acid in both the free (unbound)
> and
> > > complex (bound) aqueous states.
> > >
> > > Then if you subtract the free energy change from perturbing the free
> > > ligand, from that of perturbing the bound ligand, you should close the
> > > non-physical thermodynamic cycle and get a binding free energy.
> > >
> > > But you will need to make sure everything in your simulation is
> > > parameterised properly to get an accurate value.  You will also need to
> > > make sure you have sufficient sampling time and lambda states.
> > >
> > > Good luck!
> > >
> > > Billy
> > >
> > > On Tuesday, 5 July 2016, Alexander Alexander <
> alexanderwie...@gmail.com>
> > > wrote:
> > >
> > >> Dear gromacs user,
> > >>
> > >> I was wondering if anybody has any experience with binding free energy
> > >> calculation of a molecule (here amino acid) into a solid surface in
> > >> aqueous
> > >> solution using alchemical analysis?
> > >>
> > >> I have already tried successfully the tutorial of methane solvation
> free
> > >> energy in water and some other examples, but looks all of them are
> > >> solvation free energy and not binding free energy!
> > >>
> > >> Thanks.
> > >> Regards,
> > >> Alex
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> posting!
> > >>
> > >> * 

Re: [gmx-users] binding free energy

[Alexander Alexander]

Hello Billy,

Thanks for your response.

Please confirm me that with bonded(complex), you mean the geometry of
"amino acid+solidsurface+ water" that I should harvest in advance by normal
MD simulation in which amino acid has been absorbed into the surface. and
then this geometry should be used as the initial structure for each lambda
in order to do FEP.

Also, what do you mean please by the free (unbound)? If it is a geometry of
again "amino acid+solidsurface+ water" in which amino acid has been
solvated in water far away from the solid surface? or just an amino acid
solvated in a box of water without solid surface (amino acid + water).

Good to know that this strategy is the one mentioned in below paper (Figure
1):
http://pubs.acs.org/doi/full/10.1021/ct400487e

Here is the free energy parameter I am using in my calculation would you
please comment on it, or let me know if I should consider any other
parameter changes like mass-restrain-tempetatre-lambda?

free-energy  = yes
init-lambda-state = MYLAMBDA   ;;;from (i=0;i<15;i++)
calc-lambda-neighbors= -1
vdw-lambdas   = 0.00 0.00 0.00 0.00 0.00 0.10 0.20 0.30 0.40
0.50 0.60 0.70 0.80 0.90 1.00
coul-lambdas   = 0.00 0.25 0.50 0.75 1.00 1.00 1.00 1.00 1.00
1.00 1.00 1.00 1.00 1.00 1.00
couple-moltype= Protein_chain_A
couple-lambda0  = vdw-q
couple-lambda1  = none
couple-intramol   = no
nstdhdl  = 50
sc-alpha= 0.5
sc-coul   = no
sc-power= 1
sc-sigma= 0.3


Thanks.
Regards,
Alex




On Tue, Jul 5, 2016 at 3:03 AM, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

> Just to clarify, the formula should be:
>
>dG (bind)  = dG (complex) - dG (solv)
>
> Billy
>
> On Tuesday, 5 July 2016, Billy Williams-Noonan <
> billy.williams-noo...@monash.edu> wrote:
>
> > You would want to perturb your amino acid in both the free (unbound) and
> > complex (bound) aqueous states.
> >
> > Then if you subtract the free energy change from perturbing the free
> > ligand, from that of perturbing the bound ligand, you should close the
> > non-physical thermodynamic cycle and get a binding free energy.
> >
> > But you will need to make sure everything in your simulation is
> > parameterised properly to get an accurate value.  You will also need to
> > make sure you have sufficient sampling time and lambda states.
> >
> > Good luck!
> >
> > Billy
> >
> > On Tuesday, 5 July 2016, Alexander Alexander 
> > wrote:
> >
> >> Dear gromacs user,
> >>
> >> I was wondering if anybody has any experience with binding free energy
> >> calculation of a molecule (here amino acid) into a solid surface in
> >> aqueous
> >> solution using alchemical analysis?
> >>
> >> I have already tried successfully the tutorial of methane solvation free
> >> energy in water and some other examples, but looks all of them are
> >> solvation free energy and not binding free energy!
> >>
> >> Thanks.
> >> Regards,
> >> Alex
> >> --
> >> 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.
> >>
> >
> >
> > --
> > Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
> >
> > *LinkedIn Profile
> > <
> http://www.linkedin.com/profile/preview?locale=en_US=prof-0-sb-preview-primary-button
> >
> > **|*   +61420 382 557
> >
> > Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> > Royal Parade, Parkville, 3052
> >
> >
> >
>
> --
> Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
>
> *LinkedIn Profile
> <
> http://www.linkedin.com/profile/preview?locale=en_US=prof-0-sb-preview-primary-button
> >
> **|*   +61420 382 557
>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
> --
> Gromacs Users mailing list
>
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Re: [gmx-users] binding free energy

[Billy Williams-Noonan]

Just to clarify, the formula should be:

   dG (bind)  = dG (complex) - dG (solv)

Billy

On Tuesday, 5 July 2016, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

> You would want to perturb your amino acid in both the free (unbound) and
> complex (bound) aqueous states.
>
> Then if you subtract the free energy change from perturbing the free
> ligand, from that of perturbing the bound ligand, you should close the
> non-physical thermodynamic cycle and get a binding free energy.
>
> But you will need to make sure everything in your simulation is
> parameterised properly to get an accurate value.  You will also need to
> make sure you have sufficient sampling time and lambda states.
>
> Good luck!
>
> Billy
>
> On Tuesday, 5 July 2016, Alexander Alexander 
> wrote:
>
>> Dear gromacs user,
>>
>> I was wondering if anybody has any experience with binding free energy
>> calculation of a molecule (here amino acid) into a solid surface in
>> aqueous
>> solution using alchemical analysis?
>>
>> I have already tried successfully the tutorial of methane solvation free
>> energy in water and some other examples, but looks all of them are
>> solvation free energy and not binding free energy!
>>
>> Thanks.
>> Regards,
>> Alex
>> --
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>
>
> --
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>
> *LinkedIn Profile
> 
> **|*   +61420 382 557
>
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>
>
>

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[gmx-users] binding free energy

[Billy Williams-Noonan]

You would want to perturb your amino acid in both the free (unbound) and
complex (bound) aqueous states.

Then if you subtract the free energy change from perturbing the free
ligand, from that of perturbing the bound ligand, you should close the
non-physical thermodynamic cycle and get a binding free energy.

But you will need to make sure everything in your simulation is
parameterised properly to get an accurate value.  You will also need to
make sure you have sufficient sampling time and lambda states.

Good luck!

Billy

On Tuesday, 5 July 2016, Alexander Alexander > wrote:

> Dear gromacs user,
>
> I was wondering if anybody has any experience with binding free energy
> calculation of a molecule (here amino acid) into a solid surface in aqueous
> solution using alchemical analysis?
>
> I have already tried successfully the tutorial of methane solvation free
> energy in water and some other examples, but looks all of them are
> solvation free energy and not binding free energy!
>
> Thanks.
> Regards,
> Alex
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**|*   +61420 382 557

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Royal Parade, Parkville, 3052
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Re: [gmx-users] binding free energy

[André Farias de Moura]

Hi Alex,

if you use an alchemical method, your answer will be a complex mixture of
solvation and adsorption free energy, since the molecule may diffuse
freely, so it might be closer or farther from the surface depending on your
initial setup, simulation parameters, length of the simulation and so on.

It can be done, but I'd say the physics would always be blurred even if the
simulations were well converged. For instance, a larger box with more water
would have a larger bulk character if the surface area of the solid is kept
constant.

IMHO, you have to split the problem in two well-defined models: standard
alchemical methods should be used without the surface (providing the
solvation free energy) and a pmf calculation should be done to evaluate the
free energy profile to bring the molecule from the bulk solution to the
interface. The latter can be done by means of equilibrium distributions or
using non-equilibrium methods (umbrella sampling and steered MD).

I hope it helps.

Andre

On Mon, Jul 4, 2016 at 11:14 AM, Alexander Alexander <
alexanderwie...@gmail.com> wrote:

> Dear gromacs user,
>
> I was wondering if anybody has any experience with binding free energy
> calculation of a molecule (here amino acid) into a solid surface in aqueous
> solution using alchemical analysis?
>
> I have already tried successfully the tutorial of methane solvation free
> energy in water and some other examples, but looks all of them are
> solvation free energy and not binding free energy!
>
> Thanks.
> Regards,
> Alex
> --
> 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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Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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[gmx-users] binding free energy

[Alexander Alexander]

Dear gromacs user,

I was wondering if anybody has any experience with binding free energy
calculation of a molecule (here amino acid) into a solid surface in aqueous
solution using alchemical analysis?

I have already tried successfully the tutorial of methane solvation free
energy in water and some other examples, but looks all of them are
solvation free energy and not binding free energy!

Thanks.
Regards,
Alex
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[gmx-users] binding free energy calculation and enegy decomposition in gmx

[Marc Zhang]

Dear gromacs users group

 

I would like to calculate the binding free energy of a ligand to the
receptor and decompose the binding energy onto each residue in the pocket.

 

I have completed this task with MMPBSA. I would like to know whether gmx has
tutorial for such task using other more accurate methods.

 

Could you please suggest how I should proceed, if there is no such tutorial
avaviable.

 

Thanks a lot for your help!

 

Cheers

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[gmx-users] binding free energy

[elham tazikeh]

Dear Users
for g_mmpbsa installation (by using source code and APBS 1.4 and gromacs
4.6.7)
after below command:
pdfco@pdfco-X:~/g_mmpbsa/build$ cmake -DGMX_PATH=/opt/gromacs \
 -DAPBS14=on \
 -DAPBS_INSTALL=/opt/apbs \
 -DCMAKE_INSTALL_PREFIX=/usr/local/bin/g_mmpbsa \
 ..
i saw:

-- The C compiler identification is GNU 4.8.2
-- The CXX compiler identification is GNU 4.8.2
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
-- Generating done
-- Build files have been written to: /home/pdfco/g_mmpbsa/build

and after that by using make:
i ve got this messages:
Scanning dependencies of target energy2bfac
[ 10%] Building C object src/CMakeFiles/energy2bfac.dir/energy2bfac.c.o
Linking C executable energy2bfac
[ 10%] Built target energy2bfac
Scanning dependencies of target g_mmpbsa
[ 20%] Building C object src/CMakeFiles/g_mmpbsa.dir/main.c.o
[ 30%] Building C object src/CMakeFiles/g_mmpbsa.dir/energy_mm.c.o
[ 40%] Building C object src/CMakeFiles/g_mmpbsa.dir/InputPBSA.c.o
[ 50%] Building C object src/CMakeFiles/g_mmpbsa.dir/nsc.c.o
[ 60%] Building C object src/CMakeFiles/g_mmpbsa.dir/PbsaPrep.c.o
[ 70%] Building C object src/CMakeFiles/g_mmpbsa.dir/psize.c.o
[ 80%] Building C object src/CMakeFiles/g_mmpbsa.dir/radius.c.o
[ 90%] Building C object src/CMakeFiles/g_mmpbsa.dir/apbs14_main.c.o
[100%] Building C object src/CMakeFiles/g_mmpbsa.dir/apbs14_routines.c.o
Linking CXX executable g_mmpbsa
[100%] Built target g_mmpbsa
pdfco@pdfco-X:~/g_mmpbsa/build$ sudo make install
[sudo] password for pdfco:
[ 10%] Built target energy2bfac
[100%] Built target g_mmpbsa
Install the project...
-- Install configuration: 
CMake Error at src/cmake_install.cmake:50 (FILE):
 file cannot create directory: /usr/local/bin/g_mmpbsa/bin.  Maybe need
 administrative privileges.
Call Stack (most recent call first):
 cmake_install.cmake:37 (INCLUDE)

make: *** [install] Error 1
Also i ve got this error:

CMake Error: The source directory /home/pdfco/g_mmpbsa/build/ .. does not
exist.
Specify --help for usage, or press the help button on the CMake GUI.

i really apprciatefor any help
Sign in to reply
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Re: [gmx-users] binding free energy

[Vitaly V. Chaban]

 needs administrative privileges




On Sun, Aug 16, 2015 at 1:41 PM, elham tazikeh elham.tazi...@gmail.com wrote:
 Dear Users
 for g_mmpbsa installation (by using source code and APBS 1.4 and gromacs
 4.6.7)
 after below command:
 pdfco@pdfco-X:~/g_mmpbsa/build$ cmake -DGMX_PATH=/opt/gromacs \
 -DAPBS14=on \
 -DAPBS_INSTALL=/opt/apbs \
 -DCMAKE_INSTALL_PREFIX=/usr/local/bin/g_mmpbsa \
 ..
 i saw:

 -- The C compiler identification is GNU 4.8.2
 -- The CXX compiler identification is GNU 4.8.2
 -- Check for working C compiler: /usr/bin/cc
 -- Check for working C compiler: /usr/bin/cc -- works
 -- Detecting C compiler ABI info
 -- Detecting C compiler ABI info - done
 -- Check for working CXX compiler: /usr/bin/c++
 -- Check for working CXX compiler: /usr/bin/c++ -- works
 -- Detecting CXX compiler ABI info
 -- Detecting CXX compiler ABI info - done
 -- Configuring done
 -- Generating done
 -- Build files have been written to: /home/pdfco/g_mmpbsa/build

 and after that by using make:
 i ve got this messages:
 Scanning dependencies of target energy2bfac
 [ 10%] Building C object src/CMakeFiles/energy2bfac.dir/energy2bfac.c.o
 Linking C executable energy2bfac
 [ 10%] Built target energy2bfac
 Scanning dependencies of target g_mmpbsa
 [ 20%] Building C object src/CMakeFiles/g_mmpbsa.dir/main.c.o
 [ 30%] Building C object src/CMakeFiles/g_mmpbsa.dir/energy_mm.c.o
 [ 40%] Building C object src/CMakeFiles/g_mmpbsa.dir/InputPBSA.c.o
 [ 50%] Building C object src/CMakeFiles/g_mmpbsa.dir/nsc.c.o
 [ 60%] Building C object src/CMakeFiles/g_mmpbsa.dir/PbsaPrep.c.o
 [ 70%] Building C object src/CMakeFiles/g_mmpbsa.dir/psize.c.o
 [ 80%] Building C object src/CMakeFiles/g_mmpbsa.dir/radius.c.o
 [ 90%] Building C object src/CMakeFiles/g_mmpbsa.dir/apbs14_main.c.o
 [100%] Building C object src/CMakeFiles/g_mmpbsa.dir/apbs14_routines.c.o
 Linking CXX executable g_mmpbsa
 [100%] Built target g_mmpbsa
 pdfco@pdfco-X:~/g_mmpbsa/build$ sudo make install
 [sudo] password for pdfco:
 [ 10%] Built target energy2bfac
 [100%] Built target g_mmpbsa
 Install the project...
 -- Install configuration: 
 CMake Error at src/cmake_install.cmake:50 (FILE):
  file cannot create directory: /usr/local/bin/g_mmpbsa/bin.  Maybe need
  administrative privileges.
 Call Stack (most recent call first):
  cmake_install.cmake:37 (INCLUDE)

 make: *** [install] Error 1
 Also i ve got this error:

 CMake Error: The source directory /home/pdfco/g_mmpbsa/build/ .. does not
 exist.
 Specify --help for usage, or press the help button on the CMake GUI.

 i really apprciatefor any help
 Sign in to reply
 --
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 * Please search the archive at 
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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[gmx-users] Binding free energy of an ion from alchemical transformation

[Wojciech Kopeć]

Dear Gromacs users,

I'm thinking about performing free energy calculations for a protein that
binds cations,  using alchemical transformation method. In the simplest
case I'd transform an ion (one atom) into a naked particle; however in this
case I'd get a non-zero overall charge of the system during the charge
decoupling. I'm aware of some corrections for that and also that Gromacs
probably neutralises the charge with PME (?). Another approach I've been
thinking of is to simultaneously couple a naked particle somewhere in the
bulk with the environment, switching on the charge in a same way as the
charge of the ion is being switched off. In this way, the charge would be 0
all the time, and at the end of the simulation would yield the protein with
an empty binding site and the ion somewhere in the bulk. Are there any
obvious pitfalls with this approach?

Thank you,
Wojciech
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[gmx-users] binding Free energy

[Urszula Uciechowska]

Dear gromacs user,

I would like to calculate Binding Free Energy Calculations for my
protein-DNA complex (already run for 50ns). Is there any manual or
tutorial (for more complex systems) available?

best regards
Urszula




-
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/

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Re: [gmx-users] binding Free energy

[Justin Lemkul]

On 10/23/14 10:35 AM, Urszula Uciechowska wrote:

Dear gromacs user,

I would like to calculate Binding Free Energy Calculations for my
protein-DNA complex (already run for 50ns). Is there any manual or
tutorial (for more complex systems) available?



See published methods like g_mmpbsa (very recent) or GMXAPBS.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] binding Free energy

[Erik Marklund]

Dear Urszula,

Apologies for the self promotion, but we've made some attempts to do that for a 
TF-DNA complex: http://www.pnas.org/content/110/49/19796. Note that the 
rotational degrees of freedom are hard to sample and you may need some further 
assumptions about mesoscopic scales for the energies to be meaningful. 

Kind regards,
Erik

On 23 Oct 2014, at 15:35, Urszula Uciechowska 
urszula.uciechow...@biotech.ug.edu.pl wrote:

 Dear gromacs user,
 
 I would like to calculate Binding Free Energy Calculations for my
 protein-DNA complex (already run for 50ns). Is there any manual or
 tutorial (for more complex systems) available?
 
 best regards
 Urszula
 
 
 
 
 -
 Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
 http://www.ug.edu.pl/
 
 -- 
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 * Please search the archive at 
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
 
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Re: [gmx-users] binding Free energy

[andrea]

Hi,

thanks Justin to point out our tool GMXPBSA  (GMXAPBS was the old one)

http://www.sciencedirect.com/science/article/pii/S0010465514002240

and new version 2.1:

http://www.sciencedirect.com/science/article/pii/S0010465514003154

The link to the program is still not avaliable but you can grab it here:

http://gdriv.es/gmxpbsa

along with examples. For any help please consider to use our small 
mailing list here https://groups.google.com/forum/#!forum/gmxpbsa


Best

and

On 23/10/2014 16:50, Justin Lemkul wrote:



On 10/23/14 10:35 AM, Urszula Uciechowska wrote:

Dear gromacs user,

I would like to calculate Binding Free Energy Calculations for my
protein-DNA complex (already run for 50ns). Is there any manual or
tutorial (for more complex systems) available?



See published methods like g_mmpbsa (very recent) or GMXAPBS.

-Justin



--
---
Andrea Spitaleri PhD
Principal Investigator AIRC
D3 - Drug Discovery  Development
Istituto Italiano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
http://www.iit.it/en/d3-people/andrea-spitaleri.html
ORCID: http://orcid.org/-0003-3012-3557

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