Re: [gmx-users] Poisson-Boltzmann free energy in gromacs?

[Francesco Oteri]

Hi Sanku,
you can use APBS (Adaptive Poisson-Boltzman Solver, 
http://www.poissonboltzmann.org/apbs/ ).
This program computes the PB equation on a single conformation, but you 
can write a script to calculate values over trajectory.
APBS has the advances to be integrated into VMD and pymol, moreover is 
avalaible an MPI parallelized version.



Francesco


Il 17/07/2011 02:47, Mark Abraham ha scritto:

On 17/07/2011 10:45 AM, Justin A. Lemkul wrote:



Sanku M wrote:
I thought since the implicit solvent model has been invoked 
recently, there might be some features for PB calculation as well.




You can get GB polarization energies with the implicit solvent code, 
but not PB, as far as I am aware.  If there are undocumented 
features, perhaps one of the developers can comment.  But given the 
lack of any documentation on the matter, I would conclude that direct 
PB calculations cannot be done at present.


They can't

Mark



-Justin

 


*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Sat, July 16, 2011 7:35:43 PM
*Subject:* Re: [gmx-users] Poisson-Boltzmann free energy in gromacs?



Sanku M wrote:
> Hi,
>  I was wondering whether, in gromacs,  there is any way of 
calculating the electrostatic free energy using poisson Boltzmann 
equation.


There is no mention of such a feature in the manual, so I would 
suspect the answer is no.


-Justin

-- 

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


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[gmx-users] PDB2GMX :There are 0 donors and 0 acceptors

[ÏéÇ« ¿×]

Dear Gromacs Users,
  When I use the pdb2gmx command on my protein-DNA complex, for the A chain 
which consists of the protein.pdb2gmx told me as follows:
Processing chain 1 'A' (1222 atoms, 151 residues)
There are 243 donors and 215 acceptors
There are 285 hydrogen bonds
Will use HISE for residue 262
Identified residue ACE139 as a starting terminus.
Identified residue NME289 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
   However, for the C and D chain which consists of the DNA, it told me that 
like follows:
Processing chain 2 'C' (365 atoms, 15 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Identified residue DC1 as a starting terminus.
Identified residue DT15 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
 
   My puzzle is about the number of donors and acceptors that pdb2gmx told 
me.For protein, it seems ok,but for DNA, there none donors or acceptors. 
However, there are many oxygen or nitrogen atoms on DNA, i think they should be 
regarded as donors or acceptors.
   Therefore, why does pdb2gmx reported like that?  Does it influence the 
following simulations or trajectory analysis, such as g_hond and so on ?
Thanks in advance !
Best regards!
Xiangqian Kong



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Re: [gmx-users] PDB2GMX :There are 0 donors and 0 acceptors

[Justin A. Lemkul]

ÏéÇ« ¿× wrote:

Dear Gromacs Users,
  When I use the pdb2gmx command on my protein-DNA complex, for the A chain 
which consists of the protein.pdb2gmx told me as follows:
Processing chain 1 'A' (1222 atoms, 151 residues)
There are 243 donors and 215 acceptors
There are 285 hydrogen bonds
Will use HISE for residue 262
Identified residue ACE139 as a starting terminus.
Identified residue NME289 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
   However, for the C and D chain which consists of the DNA, it told me that 
like follows:
Processing chain 2 'C' (365 atoms, 15 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Identified residue DC1 as a starting terminus.
Identified residue DT15 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
 
   My puzzle is about the number of donors and acceptors that pdb2gmx told me.For protein, it seems ok,but for DNA, there none donors or acceptors. However, there are many oxygen or nitrogen atoms on DNA, i think they should be regarded as donors or acceptors.

   Therefore, why does pdb2gmx reported like that?  Does it influence the 
following simulations or trajectory analysis, such as g_hond and so on ?


For pdb2gmx, donors and acceptors are only relevant for determining the 
protonation state of histidine residues.  For DNA, there are no HIS, so the 
output will always show zero.  There is nothing wrong.


-Justin

--


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


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Re: [gmx-users] PDB2GMX :There are 0 donors and 0 acceptors

[Mark Abraham]

On 18/07/2011 1:41 AM, Justin A. Lemkul wrote:



ÏéÇ« ¿× wrote:

Dear Gromacs Users,
  When I use the pdb2gmx command on my protein-DNA complex, for the A 
chain which consists of the protein.pdb2gmx told me as follows:

Processing chain 1 'A' (1222 atoms, 151 residues)
There are 243 donors and 215 acceptors
There are 285 hydrogen bonds
Will use HISE for residue 262
Identified residue ACE139 as a starting terminus.
Identified residue NME289 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
   However, for the C and D chain which consists of the DNA, it told 
me that like follows:

Processing chain 2 'C' (365 atoms, 15 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Identified residue DC1 as a starting terminus.
Identified residue DT15 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully

   My puzzle is about the number of donors and acceptors that pdb2gmx 
told me.For protein, it seems ok,but for DNA, there none donors or 
acceptors. However, there are many oxygen or nitrogen atoms on DNA, i 
think they should be regarded as donors or acceptors.
   Therefore, why does pdb2gmx reported like that?  Does it influence 
the following simulations or trajectory analysis, such as g_hond and 
so on ?


For pdb2gmx, donors and acceptors are only relevant for determining 
the protonation state of histidine residues.  For DNA, there are no 
HIS, so the output will always show zero.  There is nothing wrong.


I've fixed pdb2gmx to only show this output when relevant, and to be a 
little less cryptic about what is going on :-)


Mark
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[gmx-users] Free Eerngy and Dispersion Correction

[Rainer Böckmann]

Hi All,

if switched on, is the dispersion correction included in the dH/dlambda term?

Thanks, rainer
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Re: [gmx-users] PDB2GMX :There are 0 donors and 0 acceptors

[ÏéÇ« ¿×]

Dear Justin and Mark,
  Thank you very much !

--- On Mon, 7/18/11, Mark Abraham  wrote:

> From: Mark Abraham 
> Subject: Re: [gmx-users] PDB2GMX :There are 0 donors and 0 acceptors
> To: "Discussion list for GROMACS users" 
> Date: Monday, July 18, 2011, 6:16 AM
> On 18/07/2011 1:41 AM, Justin A.
> Lemkul wrote:
> > 
> > 
> > ÏéÇ« ¿× wrote:
> >> Dear Gromacs Users,
> >>   When I use the pdb2gmx command on
> my protein-DNA complex, for the A chain which consists of
> the protein.pdb2gmx told me as follows:
> >> Processing chain 1 'A' (1222 atoms, 151 residues)
> >> There are 243 donors and 215 acceptors
> >> There are 285 hydrogen bonds
> >> Will use HISE for residue 262
> >> Identified residue ACE139 as a starting terminus.
> >> Identified residue NME289 as a ending terminus.
> >> 8 out of 8 lines of specbond.dat converted
> successfully
> >> Special Atom Distance matrix:
> >>    However, for the C and D chain which
> consists of the DNA, it told me that like follows:
> >> Processing chain 2 'C' (365 atoms, 15 residues)
> >> There are 0 donors and 0 acceptors
> >> There are 0 hydrogen bonds
> >> Identified residue DC1 as a starting terminus.
> >> Identified residue DT15 as a ending terminus.
> >> 8 out of 8 lines of specbond.dat converted
> successfully
> >> 
> >>    My puzzle is about the number of
> donors and acceptors that pdb2gmx told me.For protein, it
> seems ok,but for DNA, there none donors or acceptors.
> However, there are many oxygen or nitrogen atoms on DNA, i
> think they should be regarded as donors or acceptors.
> >>    Therefore, why does pdb2gmx reported
> like that?  Does it influence the following simulations
> or trajectory analysis, such as g_hond and so on ?
> > 
> > For pdb2gmx, donors and acceptors are only relevant
> for determining the protonation state of histidine
> residues.  For DNA, there are no HIS, so the output
> will always show zero.  There is nothing wrong.
> 
> I've fixed pdb2gmx to only show this output when relevant,
> and to be a little less cryptic about what is going on :-)
> 
> Mark
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[gmx-users] simulation of oligomers/monomers

[Kavyashree M]

Dear users,

I am working on a protein which is a dimer (in the crystal structure),
predicted according top PISA.
and some of the homologous proteins are dimers (covalent /non-covalent) some
are monomers.
There has not been any literature regarding the fact that the functional
unit is a dimer, ie the enzyme
is not functional when the dimeric interface is disturbed due to mutations.
Also the active sites are not
shared among the dimeric partners. In this situation is it meningful to do a
simulation of monomers alone
and try to get some information.

In general is it necessary to simulate only the functional oligomers or
monomer also can be done ?

Thanking you
With Regards
M. Kavyashree
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