Re: [gmx-users] Metal Ion Modelling

[Abhishek Acharya]

Hello,

Each of these models have their own merits and demerits.

Setting up bonded models are non-trivial, but as per my readings, it is
been shown to
work for alkaline and alkaline earth metal ions. So you may try this, but
getting the
correct parameters for the metal-ligand bonds is difficult.

On the other hand, non-bonded spherical model may be easier to parameterize
but i have
had mixed results with these.  Standard parameters available in various
force-fields may work,
but in some cases I have seen the ions diffuse out of the active site. In
these cases, it may
be necessary to calculate the partial charges taking the coordinating
active-site residues into
account. This requires static QM calculations.

Finally, Dummy atom model would be simpler to setup and parameters for OPLS
force-field is
available (check work by Arieh Warshel and Kamerlin). It seem promising as
it has been show
to allow correct dynamics of the protein and also supports ligand exchange
processes. But
according to my knowledge, it hasn't been used much for studying protein
dynamics as yet.

You can try both the non-bonded and dummy model and see compare the results.


Regards,
Abhishek Acharya

On Sat, Nov 11, 2017 at 4:15 PM, Quyen V. Vu  wrote:

> Dear GMX community,
> I want to simulate a long simulation of enzyme, ligands and metal cofactor
> (Mg2+), we also have NACL salt in the environment.
> I know that there are three model of metal ion: Bonded, Nonbonded, and
> Cationic Dummy atom.
> So which model for Mg2+ should I use in this case?
> Thank you in advance!
> Quyen
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Re: [gmx-users] Permeability determination

[Abhishek Acharya]

Hello,

What Justin means is that when you apply position restraints, you are
fixing the positions of the atoms. In this situation, whatever property you
calculate would be incorrect as
such a restrained system is simply unphysical; in real membranes atoms are
not restrained to a position. In your case, if you restrain the lipids and
pull your ligand through this membrane,
the natural (or simulated) dynamics of the membrane in response to ligand
pulling will be hindered. Thus the calculated PMF will be incorrect.

With respect to the first point, I don't know the details of your system,
but I think he means that in your case the movement of the membrane along
the z-axis does not matter since the system
is periodic; what matters is the relative movement of the ligand with
respect to the membrane.

I hope it is clear now.

Regards,
Abhishek Acharya


Abhishek Acharya
Research Associate,
Department of Molecular Nutrition
CSIR-Central Food Technological Research Institute,
Mysuru-570020

On Wed, Nov 15, 2017 at 11:44 AM, Chetan Puri  wrote:

> Without restraining the lipid the mdrun for pulling the ligand works but I
> am able to understand the concept which you have talked about in previous
> email.
>
>  " In a periodic system, the "center" is arbitrary as is the "sidedness" of
> the system you propose.
>
> If you restrain the lipids, you perturb their dynamics and likely influence
> the free energy of permeation across the membrane "
>
> So can you please explain in more simple way .
>
> CHETAN
>
>
> On 11/14/17 9:32 AM, Chetan Puri wrote:
>
> > I am trying to do umbrella sampling for a ligand and dopc membrane.
> > For umbrella sampling pulling step, I am unable to posre_restrain the
> > lipid, since grompp gives a error due to conflict between posre_restrain
> > file of lipid and itp file of lipid.
> > I have 128dopc molecules.
> >
> > So can someone suggest how to posre_restrain the lipid.
> >
>
> http://www.gromacs.org/Documentation/Errors?highlight=
> errors#Atom_index_n_in_position_restraints_out_of_bounds
>
> I don't think you need restraints for this kind of system, as I explained
> before, but do as you see fit.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
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Re: [gmx-users] Permeability determination

[Chetan Puri]

Without restraining the lipid the mdrun for pulling the ligand works but I
am able to understand the concept which you have talked about in previous
email.

 " In a periodic system, the "center" is arbitrary as is the "sidedness" of
the system you propose.

If you restrain the lipids, you perturb their dynamics and likely influence
the free energy of permeation across the membrane "

So can you please explain in more simple way .

CHETAN


On 11/14/17 9:32 AM, Chetan Puri wrote:

> I am trying to do umbrella sampling for a ligand and dopc membrane.
> For umbrella sampling pulling step, I am unable to posre_restrain the
> lipid, since grompp gives a error due to conflict between posre_restrain
> file of lipid and itp file of lipid.
> I have 128dopc molecules.
>
> So can someone suggest how to posre_restrain the lipid.
>

http://www.gromacs.org/Documentation/Errors?highlight=
errors#Atom_index_n_in_position_restraints_out_of_bounds

I don't think you need restraints for this kind of system, as I explained
before, but do as you see fit.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Problem in calculating static dielectric constant of Lysozymes

[Suman Das]

Thank you Prof. David for your reply and sorry for the late response. So,
now, do I have to use the original traj.xtc or still I need to do least
square fitting w.r.t the C-alpha atom and removal of translation/rotational
motion?

Thanks,
Suman

On 31/10/17 20:56, Suman Das wrote:
> > Dear Gromacs Users,
> >
>>  I am trying to calculate static dielectric constant of Lysozymes using
> > gromacs version 4.6.7. I tried to follow the protocol used earlier by
van
>>  Gunsteren (J. Phys. Chem. 1993, 97, 2009-2014).  I used PME for the
> > electrostatic interaction. First, I converted the trajectory of protein
by
> > using the command 'trjconv -f traj.xtc -o protein.xtc -pbc whole -e
> > 1000.0". Then I removed the translational and rotational motion of the
> > protein w.r.t the C-alpha atom by the following command "trjconv -f
> > protein.xtc -o protein_fit.xtc -fit rot+trans". I choose C-alpha for the
> > least square fit. And finally g_dipoles command to calculate the
dielectric
> > constant "g_dipoles -f protein_fit.xtc -o Mtot.xvg -eps epsilon.xvg -a
> > aver.xvg -d dipdist.xvg -c dipcorr.xvg". However, the dielectric
constant
> > value (1.04) that I am getting is very less compared to the actual
> > dielectric constant (30).

> Since the proteins have a net charge you have to translate them to their
> center of charge such that the leading term Q/r in Eqn 1 in the paper
> disappears (in the paper they use center of mass which is not strictly
> the same but a good approximation). The problem is that trjconv does not
> do this and therefore your net dipole moment is incorrect (since it is
> origin dependent). A roundabout way to fix this would be to compute the
> center of mass with g_traj (gmx traj) and multiply that by the total
> charge of the protein and subtract that from the dipole components. The
> compute epsilon yourself.
>
>>
> > Dipole moment (Debye)
> > -
> > Average  = 172.7138  Std. Dev. =   7.4113  Error =   0.0524
>>
> > The following averages for the complete trajectory have been calculated:
>>
> >   Total < M_x > = 38.9789 Debye
>>Total < M_y > = 54.2911 Debye
> >   Total < M_z > = -158.896 Debye
>>
>>Total < M_x^2 > = 1575.16 Debye^2
>>Total < M_y^2 > = 3006.62 Debye^2
>>Total < M_z^2 > = 25303.2 Debye^2
>>
> >   Total < |M|^2 > = 29885 Debye^2
> >   Total |< M >|^2 = 29714.9 Debye^2
>>
> >   < |M|^2 > - |< M >|^2 = 170.091 Debye^2
>>
> > Finite system Kirkwood g factor G_k = 0.00570201
> > Infinite system Kirkwood g factor g_k = 0.00561463
>>
> > Epsilon = 1.04819
>>
> > Could you help me to find out what probably went wrong with the
calculation?
>>
>>  Thanks,
>>  Suman
>>


--
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
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Re: [gmx-users] Permeability determination

[Justin Lemkul]

On 11/14/17 9:32 AM, Chetan Puri wrote:

I am trying to do umbrella sampling for a ligand and dopc membrane.
For umbrella sampling pulling step, I am unable to posre_restrain the
lipid, since grompp gives a error due to conflict between posre_restrain
file of lipid and itp file of lipid.
I have 128dopc molecules.

So can someone suggest how to posre_restrain the lipid.


http://www.gromacs.org/Documentation/Errors?highlight=errors#Atom_index_n_in_position_restraints_out_of_bounds

I don't think you need restraints for this kind of system, as I 
explained before, but do as you see fit.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Problem using gmx wham

[Jefferies D . F .]

Hi Justin, 

Thanks for your response. I've attempted to run gmx wham using GROMACS 5.1.4 
and I seem to get the same problem, even if I attempt to use dos2unix before I 
issue a command i.e.
---
Program gmx wham, VERSION 5.1.4
Source code file: 
/local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp,
 line: 1800

Fatal error:
Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I've taken a look at older posts relating to this problem, and I saw that a 
similar complaint was resolved after the poster used dos2unix (following your 
recommendation). But that hasn't seemed to work for me. 

Regards,

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: Tuesday, November 14, 2017 2:35 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem using gmx wham

At least upgrade to the latest release in the series (5.1.4) or better
yet, the actual latest version (2016.4) to see if this is a bug that's
been fixed. I seem to recall this same behavior reported before and
subsequently solved, but haven't dug it up.

-Justin

On 11/13/17 7:11 AM, Jefferies D.F. wrote:
> Hey guys,
>
> Sorry if it seems that I'm bumping this thread, but I was wondering if anyone 
> had any other suggestions before I let this thread die.
>
> Thanks.
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Jefferies 
> D.F. [dfj1...@soton.ac.uk]
> Sent: Thursday, November 02, 2017 1:29 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Problem using gmx wham
>
> Hi Justin,
>
> Thanks for the response. The .dat files were created with the vi text editor, 
> they contain lists of the .tpr and .xvg to be read, e.g.
>
> umbrella0.tpr
> umbrella1.tpr
> umbrella2.tpr
> ..
> umbrella52.tpr
>
> I've tried to use dos2unix,  i.e.
> ~> dos2unix tpr-files.dat
> and
> ~> dos2unix pullf-files.dat
>
> but I still get the same error message i.e.
>
> ---
> Program gmx wham, VERSION 5.1.2
> Source code file: 
> /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 
> 1800
>
> Fatal error:
> Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> That being said, it seems you're correct in thinking something's weird with 
> the input files. After I created new .dat files, I got this message:
>
> ---
> Program gmx wham, VERSION 5.1.2
> Source code file: 
> /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 
> 3610
>
> Fatal error:
> Found 53 file names in tpr-files.dat, but 54 in pullf-files.dat
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> gmx wham is registering 54 files, when only 53 were written.
>
>
>
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin 
> Lemkul [jalem...@vt.edu]
> Sent: Thursday, November 02, 2017 11:10 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Problem using gmx wham
>
> On 11/1/17 4:26 PM, Jefferies D.F. wrote:
>> Hi,
>>
>> I am attempting to use gmx wham to compute a potential of mean force. I have 
>> used the command line:
>>
>> gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ
>>
>> where tpr-files.dat and pullf-files.dat contain a list of the .tpr and 
>> pullf.xvg files from each umbrella sampling window, respectively.
>>
>> It seems that gmx wham is having trouble reading the .tpr and .xvg files, as 
>> I get this error message:
>>
>> ---
>>
>> Program gmx wham, VERSION 5.1.4
>>
>> Source code file: 
>> /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp,
>>  line: 1800
>>
>>
>> Fatal error:
>>
>> Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.
>>
> The extra space after "tpr" in the printed error suggests something is
> weird with the input .dat file. Did you create it with a proper plain
> text editor? What about running dos2unix on it to make sure you've got
> the right kind of line endings?
>
> -Justin
>
>> For more 

[gmx-users] Permeability determination

[Chetan Puri]

I am trying to do umbrella sampling for a ligand and dopc membrane.
For umbrella sampling pulling step, I am unable to posre_restrain the
lipid, since grompp gives a error due to conflict between posre_restrain
file of lipid and itp file of lipid.
I have 128dopc molecules.

So can someone suggest how to posre_restrain the lipid.

CHETAN
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Re: [gmx-users] GROMOS bond-stretching parameters

[Faezeh Pousaneh]

Thank you!


Best regards


On Tue, Nov 14, 2017 at 3:36 AM, Justin Lemkul  wrote:

>
>
> On 11/13/17 5:24 AM, Faezeh Pousaneh wrote:
>
>> Hi,
>> Unfortunately I do not find in Gromos literature what is the third number
>> in front of
>> bond stretching parameters, e.g 1200 below:
>> :
>>
>> ; ICB(H)[N]CB[N] B0[N]
>> #define gb_50.1230  1.6600e+07
>> ; C  - O1200
>>
>> someone please tell me,
>>
>
> It's an integer code from the original GROMOS parameter files. Note that
> it is on a comment line and thus serves no function in GROMACS.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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Re: [gmx-users] salt concentration

[Netaly Khazanov]

Indeed :)
Thank you for such detailed answer.

Have a great day!

On Tue, Nov 14, 2017 at 9:52 AM, Alex  wrote:

> I think that's high school stuff. :)
>
> N -- number of ions.
>
> V = a^3 -- volume (a is cube side length)
>
> n -- concentration (1M = 6e+26 m-3, you have 0.002 M)
>
> N = a^3*n > 1
>
> a > (1/n)^(1/3).
>
>
>
> On 11/14/2017 12:44 AM, Netaly Khazanov wrote:
>
>> It makes sense.
>> I am not sure that I follow how you calculated the critical box size
>> depending on the the concentration.
>>
>> On Tue, Nov 14, 2017 at 9:12 AM, Alex  wrote:
>>
>> It makes no difference whether you use -np/-nn or -conc. Your box is
>>> simply too small to result in a nonzero ion count with something like
>>> 0.002
>>> M. The check is rather simple: a cubic box has to be larger than
>>> (1/n)^(1/3). For 0.002 M, that critical box size is 9.4 nm.
>>>
>>> You can of course force any number of ions in there, but back-calculate
>>> the corresponding concentration, given the box volume, and you'll see
>>> that
>>> it's not what you want. This is exactly what GMX does when you call
>>> -conc.
>>>
>>> Alex
>>>
>>>
>>>
>>> On 11/13/2017 11:54 PM, Netaly Khazanov wrote:
>>>
>>> Thanks for your prompt replay.
 I thougnt it would be more elegant way to do it using the commands.
 If not that is what I am going to do.
 Best,
 Netaly

 On Mon, Nov 13, 2017 at 2:37 PM, Hermann, Johannes <
 j.herm...@lrz.tu-muenchen.de> wrote:

 Hi Netaly,

> one way would be to calculate the number of Na, Cl, and Mg ions by
> hand,
> i.e. with the box size and the respective concentrations, and add the
> correct amount of ions in two steps, with the flags -np or -nn. E.g. in
> the
> first step you add Na and Cl and in the second you add Mg.
>
> All the best
>
> Johannes
>
>
> On 13.11.2017 13:31, Netaly Khazanov wrote:
>
> Dear Gromacs User,
>
>> Is it possible to simulate system with two salt concentrations , e.g.
>> NaCl
>> 0.1 mol/L and MgCl2 0.002 mol/liter?
>>
>> The commands that i am using you can see below:
>>
>> grompp_d -f ions.mdp -c ligand_MG_box_water.gro -p topol.top -o
>> ions.tpr
>> genion_d -s ions.tpr -o ligand_box_water_NaCL.gro -p topol.top -pname
>> NA -
>> nname CL -neutral -conc 0.1
>> grompp_d -f ions.mdp -c ligand_box_water_NACL.gro -p topol.top -o
>> ions.tpr
>> genion_d -s ions.tpr -o ligand_box_water_NaCL_MgCl2.gro -p topol.top
>> -pname
>> MG -pq 2 -nname CL -neutral -conc 0.002
>>
>> The message that I got after the execution of the last command is :"No
>> ions
>> to add and no potential to calculate."
>>
>> Is it right way to do it?
>> Thank you in advance.
>> Netaly
>>
>>
>>
>> --
>>
> __
> *Technische Universität München*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl für Bioverf
> 
> ahrenstechnik
> Boltzmannstr. 15
> D-85748 Garching
> Tel: +49 8928915730
> Fax: +49 8928915714
>
> Email: j.herm...@lrz.tum.de
> http://www.biovt.mw.tum.de/
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Netaly
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mail to gmx-users-requ...@gromacs.org.