Re: [gmx-users] Fwd: how to add close proteins

[Mark Abraham]

On 23/02/2012 5:46 PM, rama david wrote:


Hi GROMACS users,
I wish to study proteins behaviour,With the help of command
 genbox -ci protein.gro -nmol .. -box 
-o  -pI am putting the four peptide
at random positions, but I need to put theem close enough so they
 are forming at least one hydrogen bond or at least enough close to
start interact  immediately with one another ..
I don´t wish to reduced by box size ...


Use editconf to rotate and translate your copies in their own coordinate 
files, and then concatenate them by hand - make sure you know how the 
file format works. Or do the foregoing in some molecule editor. Then 
solvate that.


Mark
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[gmx-users] Fwd: how to add close proteins

[rama david]

Hi GROMACS users,
I wish to study proteins behaviour,With the help of command
 genbox -ci protein.gro -nmol .. -box 
-o  -pI am putting the four peptide
at random positions, but I need to put theem close enough so they
 are forming at least one hydrogen bond or at least enough close to
start interact  immediately with one another ..
I don´t wish to reduced by box size ...
  All suggestions are appreciated for my
problem
 Thank you in advance..
Have a nice day..
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[gmx-users] interface

[mohammad agha]

Dear Mark,

Thank you very much from your reply.

Best Regards
Sara




 From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Thursday, February 23, 2012 5:24 AM
Subject: Re: [gmx-users] interface
 

On 22/02/2012 10:34 PM, mohammad agha wrote: 
Dear Mark,
>
>
>Thank you very much from your reply.
>I see a box that the half of it consists of water and another half of box is 
>void, but when I run md.mdp for production simulation all of water molecules 
>dispersed in total of box and I don't see interface and total of box filled by 
>water.
What did you expect a liquid in contact with a vacuum to do?



>
>Can you help me to construct the air/water interface, Please?
First you need to decide how you're going to produce a valid model
of *air* which is different from a *vacuum*. Then you need to find
parameters for such a model. Then it's the same kind of approach as
a mixed-solvent system (see gromacs webpage), only here it will be
mixed fluid.

Mark



>
>Best Regards
>Sara
>
>
>
>
> From: Mark Abraham 
>To: Discussion list for GROMACS users  
>Sent: Wednesday, February 22, 2012 12:59 AM
>Subject: Re: [gmx-users] interface
> 
>
>On 22/02/2012 3:11 AM, mohammad agha wrote: 
>Dear Gromacs Specialists,
>>
>>
>>I made a box consists of water with box lengths:  6nm  * 6nm  * 6nm , then I 
>>equilibrated it with NPT ensemble, box size increased to 6.66176, then I kept 
>>the x- and y-dimensions fixed, and double the system size in z as following:
>>editconf -f pr1.gro -o newbox1.gro -box 6.66176 6.66176 13.32352 -center 
>>3.33088 3.33088 3.33088
>>Next that, I placed one surfactant in center
of water phase as following:
>>editconf -f surfactant.gro -o newbox-cta.gro -box 6.66176 6.66176 13.32352 
>>-center 3.33088 3.33088 1.66544
>>genbox -cp newbox-cta.gro -cs newbox1.gro -o
newbox2.gro
>>and I added one ion to my system, then ran md.mdp for production simulation. 
>>
>>Do I have one air/water interface in my system?
>You need to use visualization software and see if the
configuration looks like you intend it to look. You
certainly don't have an air-water interface if one of
them is vacuum.
>
>Mark
>
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>
>
>

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RE: [gmx-users] Distance Restraints on Protein - possible at all?

[NG HUI WEN]

Dear Mark,

Thanks for contributing your ideas and suggestions, really appreciate it.

The reason I am playing with distance restraints on my protein is because I am 
interested to see the effects of equilibrating a protein in membrane using the 
two different restraint methods i.e. distance vs. position.

Yes, without distance restraint (i.e. removing disre = simple in the mdp) will 
allow the simulation to run to completion very smoothly.

I will give Berendsen pressure coupling a shot and see how it goes. However, 
prior to applying distance restraint on my protein, I have ran 5ns of position 
restraint simulation (with P-R coupling) and there weren't any 
complaints/problems.

Many thanks again for your help.

Cheers,
Huiwen



From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Mark Abraham
Sent: Thursday, February 23, 2012 9:48 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Distance Restraints on Protein - possible at all?

On 22/02/2012 11:17 AM, NG HUI WEN wrote:


From: NG HUI WEN
Sent: Sunday, February 19, 2012 1:19 PM
To: gmx-users@gromacs.org
Subject: Distance Restraints on Protein - possible at all?


Dear gmxusers,



I have been trying to apply distance restraints on my protein but have been 
unsuccessful thus far.

For what purpose?





I have consulted the user forum previously and with some much-appreciated help 
I have managed to get my simulation (with distance restraints applied) to run. 
However, the joy did not last long as the simulation crashed very quickly 
(after ~40-50ps).

Do they run with no restraints?

P-R P-coupling is known to be unsuitable for equilibration (see manual), so 
that might be a factor here.

Mark
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Re: [gmx-users] what restraint can I use to prevent membrane diffusion along the Z-axis?

[Mark Abraham]

On 23/02/2012 10:26 AM, Jose Borreguero wrote:

Dear GROMACS users,

While simulating a DLPC membrane, I noticed that it tends to diffuse 
along the normal (Z-axis) component. Is there a 'standard' restrain 
that is used to prevent such diffusion?
The first option I thought was to restrain the  center of mass of the 
whole membrane along the Z-axis, but I don't know what is a reasonable 
value for the force constant.
If anyone has any experience dealing with this kind of problem, please 
do reply.


Diffusion of the center of mass of the whole system is something that 
can be removed by an existing mechanism. See manual 7.3.3


Mark
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Re: [gmx-users] Adding new residue to the the force field

[Mark Abraham]

On 23/02/2012 6:02 AM, ramesh cheerla wrote:

Dear gromacs users,

   I am adding a new residue to the 
existing force field in gromacs for that i am using some new atom 
types i added these atom types to the atomtypes.atp  file  and 
ffnonbonded.itp and  I am using Buckingham potential for the 
non-bonded interactions for that i have only A,B&C values, but in the 
[atomtype] directive of the ffnonbonded.itp file one has to specify 
the  sigma and epsilon values. How can i get these values ? or can i 
specify these values as zeros ?


You will be able to use zeroes. You can verify that there's no effect by 
changing the values to ludicrous ones and observing that the simulation 
is the same.


Mark
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Re: [gmx-users] interface

[Mark Abraham]

On 22/02/2012 10:34 PM, mohammad agha wrote:

Dear Mark,

Thank you very much from your reply.
I see a box that the half of it consists of water and another half of 
box is void, but when I run md.mdp for production simulation all of 
water molecules dispersed in total of box and I don't see interface 
and total of box filled by water.


What did you expect a liquid in contact with a vacuum to do?



Can you help me to construct the air/water interface, Please?


First you need to decide how you're going to produce a valid model of 
*air* which is different from a *vacuum*. Then you need to find 
parameters for such a model. Then it's the same kind of approach as a 
mixed-solvent system (see gromacs webpage), only here it will be mixed 
fluid.


Mark



Best Regards
Sara


*From:* Mark Abraham 
*To:* Discussion list for GROMACS users 
*Sent:* Wednesday, February 22, 2012 12:59 AM
*Subject:* Re: [gmx-users] interface

On 22/02/2012 3:11 AM, mohammad agha wrote:

Dear Gromacs Specialists,

I made a box consists of water with box lengths:  6nm  * 6nm  * 6nm , 
then I equilibrated it with NPT ensemble, box size increased to 
6.66176, then I kept the /x-/ and /y-/dimensions fixed, and double 
the system size in /z as following:/
/editconf -f pr1.gro -o newbox1.gro -box 6.66176 6.66176 13.32352 
-center 3.33088 3.33088 3.33088
Next that, I placed one surfactant in center of water phase as 
following:/
/editconf -f surfactant.gro -o newbox-cta.gro -box 6.66176 6.66176 
13.32352 -center 3.33088 3.33088 1.66544

genbox -cp newbox-cta.gro -cs newbox1.gro -o newbox2.gro/
/and I added one ion to my system, then ran md.mdp for production 
simulation.

/
/Do I have one air/water interface in my system?/


You need to use visualization software and see if the configuration 
looks like you intend it to look. You certainly don't have an 
air-water interface if one of them is vacuum.


Mark

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Re: [gmx-users] Distance Restraints on Protein - possible at all?

[Mark Abraham]

On 22/02/2012 11:17 AM, NG HUI WEN wrote:


*From:*NG HUI WEN
*Sent:* Sunday, February 19, 2012 1:19 PM
*To:* gmx-users@gromacs.org
*Subject:* Distance Restraints on Protein - possible at all?

Dear gmxusers,

I have been trying to apply distance restraints on my protein but have 
been unsuccessful thus far.




For what purpose?

I have consulted the user forum previously and with some 
much-appreciated help I have managed to get my simulation (with 
distance restraints applied) to run. However, the joy did not last 
long as the simulation crashed very quickly (after ~40-50ps).




Do they run with no restraints?

P-R P-coupling is known to be unsuitable for equilibration (see manual), 
so that might be a factor here.


Mark

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[gmx-users] what restraint can I use to prevent membrane diffusion along the Z-axis?

[Jose Borreguero]

Dear GROMACS users,

While simulating a DLPC membrane, I noticed that it tends to diffuse along
the normal (Z-axis) component. Is there a 'standard' restrain that is used
to prevent such diffusion?
The first option I thought was to restrain the  center of mass of the whole
membrane along the Z-axis, but I don't know what is a reasonable value for
the force constant.
If anyone has any experience dealing with this kind of problem, please do
reply.

Best regards,
Jose M. Borreguero
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[gmx-users] Adding new residue to the the force field

[ramesh cheerla]

Dear gromacs users,

   I am adding a new residue to the existing
force field in gromacs for that i am using some new atom types i added
these atom types to the atomtypes.atp  file  and ffnonbonded.itp and  I am
using Buckingham potential for the non-bonded interactions for that i have
only A,B&C values, but in the [atomtype] directive of the ffnonbonded.itp
file one has to specify the  sigma and epsilon values. How can i get these
values ? or can i specify these values as zeros ?
Any help will be highly appreciated

Thank you


Regards,
Ramesh
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[gmx-users] Protein transition from active to passive state

[Rafał Urniaż]

> Dear Gromacs Users,
>
> I am interested in opportunities to simulate protein transition from active 
> to passive state.
> Exists a possibility to put into Gromacs two states of protein and forced the 
> transition from
> state A to B? Measuring by the way the energy of the frame state? I will be 
> thanks for 
> any suggestions, tutorials or publications to read. 
>
> Best regards
> Rafal

Dear Gromacs Users,

I am interested in opportunities to simulate protein transition from active
to passive state.
Exists a possibility to put into Gromacs two states of protein and forced
the transition from
state A to B? Measuring by the way the energy of the frame state? I will be
thanks for 
any suggestions, tutorials or publications to read. 

Best regards
Rafal



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Re: [gmx-users] Umbrella Sampling - spacing

[Steven Neumann]

Thank you!

On Wed, Feb 22, 2012 at 4:08 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>> Dear Gmx Users, Dear Justin,
>>  I run pulling of my ligand away from my protein. Then I used Justin perl
>> script to extract distances for umbrella sampling windows between my ligand
>> and crucial residue of my protein (Isoleucine). The number of hydrogen
>> bonds between ligand and protein during the pulling is app. 3 at the
>> begining, then 4 in some frames and then obviously zero (when ligand
>> dissociated).
>> Would you use the 1st frame as a starting window when number of hbonds is
>> 3 or further window when this is number is 4?
>>
>
> Assuming the first frame represents a fully-bound configuration, you
> should start there.  I'm guessing you're trying to determine the DeltaG of
> binding for your ligand.  If you define an arbitrary reaction coordinate,
> you get an arbitrary answer.  Starting and ending points dictate the value
> of DeltaG (since it is a state function).
>
>
> Is spacing of 0.2 nm (pulling of app 6 nm) sufficent for the system where
>> interactions are via hydrogen bonds and hydrophobic interactions only?
>>
>>
>
> Most systems interact via hydrogen bonds and hydrophobic interactions.
> Generally, 0.2 nm is a decent starting point, but should by no means be
> viewed as any sort of universal standard.  It worked for me in my tutorial,
> it may not work for others.  Consult the literature for similar systems and
> proceed.  If you find under-sampled regions along the reaction coordinate,
> it is trivial to add a new window.
>
> -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] Umbrella Sampling - spacing

[Justin A. Lemkul]

Steven Neumann wrote:

Dear Gmx Users, Dear Justin,
 
I run pulling of my ligand away from my protein. Then I used Justin perl 
script to extract distances for umbrella sampling windows between my 
ligand and crucial residue of my protein (Isoleucine). The number of 
hydrogen bonds between ligand and protein during the pulling is app. 3 
at the begining, then 4 in some frames and then obviously zero (when 
ligand dissociated).
Would you use the 1st frame as a starting window when number of hbonds 
is 3 or further window when this is number is 4?


Assuming the first frame represents a fully-bound configuration, you should 
start there.  I'm guessing you're trying to determine the DeltaG of binding for 
your ligand.  If you define an arbitrary reaction coordinate, you get an 
arbitrary answer.  Starting and ending points dictate the value of DeltaG (since 
it is a state function).


Is spacing of 0.2 nm (pulling of app 6 nm) sufficent for the system 
where interactions are via hydrogen bonds and hydrophobic interactions only?
 


Most systems interact via hydrogen bonds and hydrophobic interactions. 
Generally, 0.2 nm is a decent starting point, but should by no means be viewed 
as any sort of universal standard.  It worked for me in my tutorial, it may not 
work for others.  Consult the literature for similar systems and proceed.  If 
you find under-sampled regions along the reaction coordinate, it is trivial to 
add a new window.


-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] Umbrella Sampling - spacing

[Steven Neumann]

Dear Gmx Users, Dear Justin,

I run pulling of my ligand away from my protein. Then I used Justin perl
script to extract distances for umbrella sampling windows between my ligand
and crucial residue of my protein (Isoleucine). The number of hydrogen
bonds between ligand and protein during the pulling is app. 3 at the
begining, then 4 in some frames and then obviously zero (when ligand
dissociated).
Would you use the 1st frame as a starting window when number of hbonds is 3
or further window when this is number is 4?
Is spacing of 0.2 nm (pulling of app 6 nm) sufficent for the system where
interactions are via hydrogen bonds and hydrophobic interactions only?

Thank you.

Steven
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[gmx-users] g_dist lifetime option

[Markus Weingarth]

Dear gromacs users,I have a comprehension question to g_dist with the lifetime(-lt) option.I want to determine the lifetime of a certain sidechain - ion contact (I use all ions as a group) within a radis of 0.6 nm.output:@    title "a_538 - K within 0.6 nm"@    xaxis  label "Time (ps)"@    yaxis  label "Number of contacts"@TYPE xy 0.000  1.183   200.000  1.088   400.000  1.048   600.000  1.024   800.000  1.000  1000.000  0.975  1200.000  0.958  1400.000  0.941  1600.000  0.924  1800.000  0.906  2000.000  0.888  2200.000  0.870  2400.000  0.851  2600.000  0.832  2800.000  0.812  3000.000  0.793  3200.000  0.773  3400.000  0.752etc.I have difficulties in understanding why the number of contacts decreases to below zero, though at least one ion is constantly within a raidus of 0.6 nm. Is this a correlation function? Is it possible to look up how this is calculated here?this says the help option :With options -lt and -dist the number of contacts
of all atoms in group 2 that are closer than a certain distance
to the center of mass of group 1 are plotted as a function of the time
that the contact was continously present.Thank you very much.Markus  Ihr WEB.DE Postfach immer dabei: die kostenlose WEB.DE Mail App für iPhone und Android.   https://produkte.web.de/freemail_mobile_startseite/

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Re: [gmx-users] Protonation state of the ionisable residues

[Justin A. Lemkul]

James Starlight wrote:

Thanks Justin.

Your aproach is very usefull indeed.

I've just one relative question about CAPPING of the termi in the case 
of simulation of the membrane receptors. In that proteins both of N and 
C termi are in the water polar layer. In the literature I've  found 
nothing about capping of the termi as well as changing of protonated 
state of that fragments. What advantages might have such capping of the 
termni of that protein?




Probably none.  If termini are exposed to solvent, they are generally assumed to 
be in their predominant (ionized) form.  Capping is typically used when a 
polypeptide fragment is being modeled, such that residues that are normally 
present at the N- or C-termini are not present in the simulation.  Neutralizing 
the charges by adding amide caps is a more realistic representation in such cases.


-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] Internal water in the membrane receptor

[James Starlight]

Dear Gromacs Users!

I want to perform simulation of the membrane receptor in the membtane
environment. There are some evidence about precense of the
functional-relevant internal water mollecules in the transmembrane
alpha-helix bundle of the receptor.


I want to take into account that internal water in my model. I have
coordinates of the X-ray structures wich have all that water. Also I have
perfect model of the same protein wich have not that water but have
full-length structure ( there are some missing residues in the X-ray
structures- e.g in the loop regions).

So what the best way to build system would  be in my case?

1-  Should I use X-ray structure where internal water has already present
and build missing loops via model software ? How I could preserve the
internal waters in that starting structure when this structure will be
processed by pdb2gmx ?

2- Or the best way is to incorporate all waters in the model of my protein
? If this aproach could be better what is the simplest way to transfer
exact coordinates of water in that holo model ? )

Thanks for help


James
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Re: [gmx-users] Protonation state of the ionisable residues

[James Starlight]

Thanks Justin.

Your aproach is very usefull indeed.

I've just one relative question about CAPPING of the termi in the case of
simulation of the membrane receptors. In that proteins both of N and C
termi are in the water polar layer. In the literature I've  found nothing
about capping of the termi as well as changing of protonated state of that
fragments. What advantages might have such capping of the termni of that
protein?


James

2012/2/22 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>> Dear Gromacs Users!
>>
>>
>>
>> I'd like to change default protonation state of some specified Glu and
>> Asp residues im my protein.
>>
>> By defaylt pdb2gmx -ignh create unprotonated state of the negatively
>> charged residues but I want to make 2 of such residues protonated to mimick
>> some intermollecular interactions.
>>
>> How I could make such edition to my structure ? Is it possible to make
>> such changing AFTER pdb2gmx processing of my structure ( manually editiong
>> GRO or PDB file and TOPOLOGY)?
>>
>>
> It is possible, but would be an extreme hassle and would be very
> error-prone. You'd have to add in the new atoms, renumber *all* subsequent
> bonded and nonbonded interactions.
>
> The better approach is to re-create the topology with pdb2gmx -asp -glu.
>
> -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] Protonation state of the ionisable residues

[Justin A. Lemkul]

James Starlight wrote:

Dear Gromacs Users!



I'd like to change default protonation state of some specified Glu and 
Asp residues im my protein.


By defaylt pdb2gmx -ignh create unprotonated state of the negatively 
charged residues but I want to make 2 of such residues protonated to 
mimick some intermollecular interactions.


How I could make such edition to my structure ? Is it possible to make 
such changing AFTER pdb2gmx processing of my structure ( manually 
editiong GRO or PDB file and TOPOLOGY)?




It is possible, but would be an extreme hassle and would be very error-prone. 
You'd have to add in the new atoms, renumber *all* subsequent bonded and 
nonbonded interactions.


The better approach is to re-create the topology with pdb2gmx -asp -glu.

-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] R: Re: several questions about g_hbond -contact

[Anna Marabotti]

 
Dear Justin,
thakn you for your answer, although it is quite discouraging...

g_mindist is only partially suitable for my scope: it gives me the number of
contacts, and also the residues that contact the ligand at least once in the
simulation (if I use -or in addition to -od), but with g_hbond I obtained a
matrix of contacts and I could do another analysis using your plot_hbmap.pl
script. g_mindist does not produce the matrix, therefore I don't know the %
of time that a contact is present between protein and ligand (which was
rather useful for my scope).

Any other comment about this subject? (especially from developers) As I told
before, I'm not able to go into the code and see what -r2 does, but people
who wrote the code should be the ones who know this answer, I presume...

Thanks
Anna

--

Message: 1
Date: Tue, 21 Feb 2012 15:39:48 -0500
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] several questions about g_hbond -contact
To: Discussion list for GROMACS users 
Message-ID: <4f440114.9010...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Anna Marabotti wrote:
> Dear users,
> I'm using g_hbond with option -contact in order to find the contacts 
> between my protein and a series of ligands, in a radius of 0.5 nm. I 
> made several calculations but I'm quite uncertain about the results, 
> therefore I'm asking you some questions.
>  
> The command I used is:
> g_hbond -f my_prot.xtc -s my_prot.tpr -n index.ndx -g logfile.log -num 
> contact_num.xvg -hbn contact.ndx -hbm contact.xpm -contact (for options 
> -r and -r2 see below).
>  
> Here my questions:
> 1) I have to indicate two groups when prompted. If I select first "1" 
> (protein) and then "15" (ligand), the program does not find contacts (it 
> calculates, but says "No contacts found"). On the contrary, if I first 
> select "15" and then "1", the program finds contacts. Why? I'm expecting 
> that if an atom of the protein contacts an atom of the ligand, it is a 
> reversible thing, especially because this is not a H-bond in which the 
> different order D-A could affect the results.
> To proceed with my test, I always selected first "15" and then "1".
>  
> 2) If I fix only -r 0.5, the program starts calculating. It finds a 
> number of "donor" and "acceptor" atoms and starts doing a grid search on 
> a 18x18x13 grid, with rcut=0.5. It calculates for all the frames of the 
> trajectory, then at the end it finds a number of "hbonds" and 0 
> different atom-pairs within H-bond distance. At the end, I obtain a 
> range checking error: "Variable y has value 0. It should have been 
> within [ 0 .. 0 ] and the files .xvg, .log and .ndx are created, but the 
> file .xpm is not.
> If I understand well, the -r2 flag is then absolutely necessary to tell 
> the program that it does not have to treat this as an H-bond search, but 
> as a contact search, right? The -contact flag is not sufficient, alone?
>  
> 3) If I fix -r 0.5 -r2 0.6, the program starts calculating. It finds the 
> same number as above of "donor" and "acceptor" atoms and starts doing a 
> grid search on a 15x15x11 grid with rcut=0.6. It calculates for all the 
> frames of the trajectory, then at the end it finds a number of 
> "contacts" and a number of different atom-pairs within second cutoff 
> distance. It produces all the files (.xvg, .ndx, .log and .xpm).
> In this case, the program has indeed calculated the "contacts", instead 
> of the "hbonds". However, I don't understand if it calculates the 
> contacts within a cutoff distance of 0.5 or within a cutoff distance of 
> 0.6 nm. If I change this second value to, say, 1 nm, the number of 
> contacts is still the same, but the number of different atom-pairs 
> increases to 15951, and the grid has different dimensions (9x9x6)
> In this case, my question is: how the -r2 flag affects the number of 
> contacts to find? (I would like to ask: what is the function of flag 
> -r2? but looking at the gmx-users archive, it seems to me that nobody 
> knows it...and I'm not able to look into the code, as suggested by 
> somebody...)
>  

All of the above are valid points.  These features have little or no 
documentation (there is an open redmine issue about this).  I find the
g_hbond 
code hopelessly confusing, myself.

> My final question is, obviously: what is the correct command to provide 
> to obtain what I want, i.e. the number of contacts between the protein 
> and the ligand within a cutoff radius of 0.5 nm?
>  

Don't use g_hbond at all.

g_mindist -d 0.5 -on

-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] interface

[mohammad agha]

Dear Mark,

Thank you very much from your reply.
I see a box that the half of it consists of water and another half of box is 
void, but when I run md.mdp for production simulation all of water molecules 
dispersed in total of box and I don't see interface and total of box filled by 
water.

Can you help me to construct the air/water interface, Please?

Best Regards
Sara




 From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Wednesday, February 22, 2012 12:59 AM
Subject: Re: [gmx-users] interface
 

On 22/02/2012 3:11 AM, mohammad agha wrote: 
Dear Gromacs Specialists,
>
>
>I made a box consists of water with box lengths:  6nm  * 6nm  * 6nm , then I 
>equilibrated it with NPT ensemble, box size increased to 6.66176, then I kept 
>the x- and y-dimensions fixed, and double the system size in z as following:
>editconf -f pr1.gro -o newbox1.gro -box 6.66176 6.66176 13.32352 -center 
>3.33088 3.33088 3.33088
>Next that, I placed one surfactant in center of water
phase as following:
>editconf -f surfactant.gro -o newbox-cta.gro -box 6.66176 6.66176 13.32352 
>-center 3.33088 3.33088 1.66544
>genbox -cp newbox-cta.gro -cs newbox1.gro -o newbox2.gro
>and I added one ion to my system, then ran md.mdp for production simulation. 
>
>Do I have one air/water interface in my system?
You need to use visualization software and see if the configuration
looks like you intend it to look. You certainly don't have an
air-water interface if one of them is vacuum.

Mark

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[gmx-users] interface

[mohammad agha]

Dear Dr. Warren,

Thank you very much from your response. 

When I see the coordinate file, there is a box consists of water in half of it 
and another half of box is void, but when I do md.mdp for production 
simulation, all of water molecules are dispersed in total of box.

Can you help me for construct the air/water interface, Please?

Best Regards
Sara




 From: Dallas Warren 
To: Discussion list for GROMACS users  
Sent: Wednesday, February 22, 2012 4:26 AM
Subject: RE: [gmx-users] interface
 

 
What does it look like when you visualise the coordinate file?  That is how you 
can answer that question, as we certainly can’t.
 
And as you will soon find out, you cannot have a single interface in a 
simulation box, you have to have two.
 
Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.
 
From:gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of mohammad agha
Sent: Wednesday, 22 February 2012 3:12 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] interface
 
Dear Gromacs Specialists,
 
I made a box consists of water with box lengths:  6nm  * 6nm  * 6nm , then I 
equilibrated it with NPT ensemble, box size increased to 6.66176, then I kept 
the x- and y-dimensions fixed, and double the system size in z as following:
editconf -f pr1.gro -o newbox1.gro -box 6.66176 6.66176 13.32352 -center 
3.33088 3.33088 3.33088
Next that, I placed one surfactant in center of water phase as following:
editconf -f surfactant.gro -o newbox-cta.gro -box 6.66176 6.66176 13.32352 
-center 3.33088 3.33088 1.66544
genbox -cp newbox-cta.gro -cs newbox1.gro -o newbox2.gro
and I added one ion to my system, then ran md.mdp for production simulation. 
Do I have one air/water interface in my system?
Please help me.
 
Best Regards
Sara
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[gmx-users] Release of the R.E.D. III.5 tools

[FyD]

Dear All,

 We are pleased to announce the release of the program RESP ESP  
charge Derive version III.5 (or R.E.D. III.5) and its related tools  
(Ante_R.E.D.-1.5 and X R.E.D. III.5) available @  
http://q4md-forcefieldtools.org/RED/.


 New features available:
 - Bug corrections and code cleaning,
 - Update of the Mini-HowTo & Tutorials,
 - Better handling of Gaussian, GAMESS and Firefly error messages,
 - Charge value rounding off errors automatically corrected at 10-6  
up to 10-2 depending on the user choice,
 - Handling geometrical constraints in the P2N file format (geometry  
optimization using the Gaussian program),

 - Two new scripts for data submission in R.E.DD.B.,
 - New version for the RESP program: version 2.2 with updated documentation.

 The R.E.D. III.5 tools are distributed under the GNU General Public  
License after a simple Register & Download procedure.


 The article describing the R.E.D. tools is available @  
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/.


 News about the latest developments of R.E.D. IV can be found @  
http://q4md-forcefieldtools.org/RED/popup/news.php.


 RESP and ESP charge derivation for a new structure is an important  
step in molecular dynamics simulations based on AMBER, CHARMM, GLYCAM  
and OPLS force fields. To derive such atom-centered charges three  
steps need to be followed:
 - First, the molecule studied is optimized to determine a stable  
minimum (using a quantum chemistry software).
 - Then, this minimized structure is used to calculate a Molecular  
Electrostatic Potential (MEP) on a three-dimensional grid (using again  
a quantum chemistry software).
 - Finally, this grid is exported into the 'RESP program' (also  
downloadable from the CCL software database or from  
q4md-forcefieldtools) which is used to fit atom-centered charges to  
the MEP.


 Although this method is now used 'routinely' to obtain partial  
charges for molecules, in our opinion, it suffers from a number of  
limitations:
 - To apply this strategy, which requires the described above steps  
but also numerous format conversions between the different programs  
used, a significant number of scripts, programs and compilers are  
needed and used sequentially. Consequently, the procedure is tedious,  
time-consuming, and numerous errors can be introduced without having a  
real way to check them.
 - Although it is admitted that any quantum chemistry programs could  
be used to minimize the starting structure and to calculate the MEP,  
the 'Amber' developers mainly use the 'Gaussian' program, which is a  
proprietary software. The 'GAMESS' academic program, which is provided  
at no cost and which provide similar functionality for 'RESP' and  
'ESP' charges development than 'Gaussian', is not officially used to  
derive 'RESP' or 'ESP' charges. Indeed, it is known that partial  
charges calculated using 'GAMESS', are 'different' than those  
determined using 'Gaussian'.
 - Finally, starting from different sets of Cartesian coordinates for  
a same molecule, the 'RESP' or 'ESP' partial charges are, in somes  
cases, not reproducible even using 'Gaussian', making errors in the  
protocol difficult to detect.



 Thus, we developed the R.E.D. I (RESP ESP charge Derive, version  
1.0) program to automatically derive 'RESP' and 'ESP' charges starting  
from an un-optimized PDB structure. R.E.D. sequentially executes (i)  
either the 'GAMESS' program or the 'Gaussian' program to minimize the  
target structure and to compute the corresponding MEP, and (ii) the  
'RESP' program to fit the atom-centered charges to the grid previously  
determined. Format conversions needed during the procedure and  
'GAMESS', 'Gaussian' and 'RESP' inputs are automatically generated by  
R.E.D. By controlling the molecular orientation of the optimized  
geometry, a new RESP fitting procedure based on multi-orientation  
feature is proposed and results in highly reproducible 'RESP' and  
'ESP' charges independently of the QM software or the initial  
Cartesian coordinate set.


 With R.E.D. II (version 2.0), multi-conformation RESP and ESP fit  
has been implemented. Such an approach permits to make the atom charge  
values more 'general', and is useful in molecular dynamics simulations  
where the whole conformational space needs to be explored. Thus with  
R.E.D.-II, 'multi-conformation' and 'multi-orientation' RESP fit can  
be performed together or independently according to the user choice.  
'Standard' but also 'non-standard' RESP inputs can also be generated.  
Finally, RESP and ESP charges can be derived for chemical elements  
having up to a total number of electrons, Z = 35.


 With R.E.D. III.x (version 3.x), the control of charge constraints  
for atoms and groups of atoms in a molecule (intra-molecule charge  
constraint) or between two molecules (inter-molecule charge constraint  
and inter-molecular charge equivalencing) has been incorporated  
allowing for the derivation of the 

Re: [gmx-users] COMPASS force field revisited Bond Dihedral and Angle Dihedral cross terms

[David van der Spoel]

On 2012-02-21 23:26, Broadbent, Richard wrote:




On 21/02/2012 19:02, "David van der Spoel"  wrote:


On 2/21/12 6:17 PM, Richard Broadbent wrote:

Dear All,

I am considering conducting a simulation of a polymeric system in
gromacs. I would like to use the COMPASS forcefield as it has a complete
parameter set for my molecule.

I believe the majority of the implementation is simple (though long and
fiddly). However, it has Bond-Dihedral and Angle-Dihedral cross terms.
These terms are not listed in either Chapter 4 or 5 of the Manual. Which
leads me to believe that they are not implemented. However CMAP
dihedrals are not documented in chapters 4&   5 and they are implemented
in the code. I therefore had a quick look in src/gmxlib/ifunc.c and
couldn't see those terms. However, my knowledge of the layout of the
source code is extremely limited so I could be looking in the wrong
place, and thought it best to ask.

Are Bond-Dihedral and Angle-Dihedral cross terms available in gromacs
4.5.5?


What do the functions look like?


Bond dihedral:
(b-b0)*[k_1*cos(phi) +k_2*cos(2*phi)+k_3*cos(3*phi)]

Angle Dihedral:
(theta -theta_0)*[k_1*cos(phi) +k_2*cos(2*phi)+k_3*cos(3*phi)]

There is also angle-angle-dihedral:
k*(theta -theta_0)*(theta' -theta_0')*cos(phi)


For this to work, the best would be to implement a new dihedral 
function. Due to the way this works the function would need quite a few 
parameters though.


atoms i,j,k,l
3 b0 for i,j and j,k and k,l
2 theta_0 for i,j,k and j,k,l
k_1, k_2, k_3 (shouldn't there be a k_0)?

In all 8-9 parameters! What also is unfortunate is that a number of 
these parameters are most likely repeats (b0, theta_0) from other lists. 
One could of course combine bonds, angles and dihedrals into one monster 
routine, but then dealing with constraints becomes somewhat harder again.


By the way this thread now should be moved to the developer list I guess.



Most likely they are not implemented though if they're not in the manual.







Thanks,

Richard








--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] mdrun on GROMACS 3.3.1

[francesca vitalini]

Hi,
sorry I'm back to this thread after quite a long time, as I was trying
to solve other problems. Now I'm back to the reverse transformation
tutorial on the martini webpage and whenever I try to use the mdp
script provided there for the annealing I just end up with the same
error message, which is that it cannot open the .xtc file that it is
supposed to create.

Program mdrun, VERSION 3.3.1
Source code file: gmxfio.c, line: 706

Can not open file:
annealing_LLL_frag.xtc
---

"Love is Like Moby Dick, Get Chewed and Get Spat Out" (Urban Dance Squad)

Halting program mdrun

gcq#83: "Love is Like Moby Dick, Get Chewed and Get Spat Out" (Urban
Dance Squad)

--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

The mdp file looks like


cpp =  /lib/cpp
constraints =  none
integrator  =  md
tinit   =  0.0
dt  =  0.002
nsteps  =  4
nstcomm =  0
nstxout =  1
nstvout =  1
nstfout =  1
nstlog  =  1
nstenergy   =  100
nstxtcout   =  100
xtc_precision   =  1000
nstlist =  10
energygrps  =  Protein Water
ns_type =  grid
rlist   =  0.9
coulombtype =  Generalized-Reaction-Field
epsilon_rf   = 62
rcoulomb=  1
rvdw=  1.0
Tcoupl  =  nose-hoover
tc-grps =  Protein Water
ref_t   =  300  300
tau_t   =  0.1  0.1
Pcoupl  =  no
table_extension =  1.2


;dihre   =  simple ; Some dihedrals are restrained  for
instance peptide bonds are set to trans conformation.
;dihre_fc=  500
;dihre_tau   =  0.0
;nstdihreout =  50

cap_force= 15000
cap_a= 100
fc_restr = 12000
r_CGW= 0.21
fc_restrW= 400

rel_steps= 0
rel_water= no


andersen_seed   =  815131
annealing   =  single single
annealing_npoints   =  2 2
annealing_time  =  0 60  0 60 ; CHANGE HERE -annealing control
points for each group
annealing_temp  =  1300 300 400 300  ; list of temperatures at
control points for each group


gen_vel = yes
gen_temp= 1300
gen_seed= 473529
lincs_warnangle = 100

Compared to the file of the tutorial I just have changed the number of
groups (2 instead of 3) and the rest is as the one that is provided,
so I really don't understand why is GROMACS 3.3.1 complaining.
Can you help me on that?
Thanks a lot



2012/1/31 Justin A. Lemkul :
>
>
> francesca vitalini wrote:
>>
>> Well I'm keeping struggling with this script. Apparently the problem in in
>> using the integrator md with the GOMACS 3.3.1 version. In fact the same .mdp
>> file with integrator steep works. while with md it always gives the error
>> message that it cannot open the .xtc file.
>
>
> The md integrator can produce an .xtc file, steepest descent EM does not.
>
>
>> How can I get around this problem?
>> I can only see two ways now:
>> -either there is a way to use md with GROMACS 3.3.1
>> -or there is a way so that the mdrun of a newer version of GROMACS can
>> deal with the file. If I try, even specifying the path for each .itp file,
>> then the program cannot find certain atomtypes, such as
>> Atomtype CH2R not found
>> any suggestions here?
>
>
> Some renaming has occurred for some atomtypes, and the force fields have
> been re-organized in a more sensible fashion in newer versions.  For
> instance, the CH2R atom type in the Gromos96 force fields is now called
> CH2r.
>
> -Justin
>
>> Thanks
>> Francesca
>>
>>
>>
>> 2012/1/31 Francesca Vitalini > >
>>
>>
>>    Thank you Justin for your quick reply. Unfortunately I cannot use a
>>    more modern version of GROMACS as my topology and .gro files where
>>    first created for a reverse transformation from cg   to fg and thus
>>    required the 3.3.1 version and some specific .itp files that are
>>    only present in that version. If I try to run it all with GORMACS
>>    4.5 that it crashes immediately.
>>    I've also tried without the -cpo option but it doesn't change anything.
>>    I've checked the permission on the folder and as I supposed I have
>>    total access to it so it might not effect the results.
>>    If I open with vi a file with the same name as the .xtc file that I
>>    need for the script and write in it some crap just to try and then I
>>    just re run the mrdun command I don't get the error message anymore
>>    but gromacs compla

Re: [gmx-users] trjconv -dump problem

[Peter C. Lai]

Dunno but try with -timestep 1?

Anyway, the .gro file emitted by mdrun contains the last frame anyway,
so there's not much reason to use trjconv to dump the last frame in the 
first place...

On 2012-02-13 04:19:45PM +0200, Ehud Schreiber wrote:
> Dear Gromacs users,
> 
>  
> 
> I minimized a protein structure 1IARcompleted_WT.pdb, getting, among
> others, the files 1IARcompleted_WT_minimized.trr and
> 1IARcompleted_WT_minimized_potential_energy.xvg . Looking at the latter
> file showed the last frame to be at 217 ps:
> 
>  
> 
> .
> 
> .
> 
> @ s0 legend "Potential"
> 
> 0.00  -31997.519531
> 
> 0.00  -33810.406250
> 
>   200.00  -69850.609375
> 
>   217.00  -69898.031250
> 
>  
> 
> I wanted to extract only this last frame from the .trr file, so used
> 
>  
> 
> trjconv  -f 1IARcompleted_WT_minimized.trr -o
> 1IARcompleted_WT_minimized_217.trr -dump 217
> 
>  
> 
> However, this seems to have produced a file with the t = 200 ps
> conformation, though the dump parameter was recorded, as trjconv output
> was:
> 
>  
> 
> .
> 
> .
> 
> Option   Type   Value   Description
> 
> --
> 
> .
> 
> .
> 
> -dumptime   217 Dump frame nearest specified time (ps)
> 
> .
> 
> .
> 
> Will write trr: Trajectory in portable xdr format
> 
> trn version: GMX_trn_file (single precision)
> 
> Reading frame   2 time  200.000   
> 
> Dumping frame at t= 200 ps
> 
> Reading frame   3 time  217.000   
> 
> .
> 
> .
> 
>  
> 
> Also, using -dump 200 gave an identical file to the above.
> 
>  
> 
> Any idea why the expected timeframe isn't reproduced?
> 
> I'm using gromacs 4.5.3.
> 
>  
> 
> Thanks,
> 
> Ehud Schreiber.
> 
>  
> 

> -- 
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-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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[gmx-users] trjconv -dump problem

[Ehud Schreiber]

Dear Gromacs users,

 

I minimized a protein structure 1IARcompleted_WT.pdb, getting, among
others, the files 1IARcompleted_WT_minimized.trr and
1IARcompleted_WT_minimized_potential_energy.xvg . Looking at the latter
file showed the last frame to be at 217 ps:

 

.

.

@ s0 legend "Potential"

0.00  -31997.519531

0.00  -33810.406250

  200.00  -69850.609375

  217.00  -69898.031250

 

I wanted to extract only this last frame from the .trr file, so used

 

trjconv  -f 1IARcompleted_WT_minimized.trr -o
1IARcompleted_WT_minimized_217.trr -dump 217

 

However, this seems to have produced a file with the t = 200 ps
conformation, though the dump parameter was recorded, as trjconv output
was:

 

.

.

Option   Type   Value   Description

--

.

.

-dumptime   217 Dump frame nearest specified time (ps)

.

.

Will write trr: Trajectory in portable xdr format

trn version: GMX_trn_file (single precision)

Reading frame   2 time  200.000   

Dumping frame at t= 200 ps

Reading frame   3 time  217.000   

.

.

 

Also, using -dump 200 gave an identical file to the above.

 

Any idea why the expected timeframe isn't reproduced?

I'm using gromacs 4.5.3.

 

Thanks,

Ehud Schreiber.

 

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[gmx-users] Protonation state of the ionisable residues

[James Starlight]

Dear Gromacs Users!



I'd like to change default protonation state of some specified Glu and Asp
residues im my protein.

By defaylt pdb2gmx -ignh create unprotonated state of the negatively
charged residues but I want to make 2 of such residues protonated to mimick
some intermollecular interactions.

How I could make such edition to my structure ? Is it possible to make such
changing AFTER pdb2gmx processing of my structure ( manually editiong GRO
or PDB file and TOPOLOGY)?


Thanks

James
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Re: [gmx-users] Re: Placing ions in the specified positions

[Peter C. Lai]

Your starting topology is already broken if you have a non-integral total 
charge that's larger than the magnitude for floating point errors (in your
case, .02 is floating point error, the 0.55 is systematic). Try figuring 
out where the charge assignments went wrong (the qtot column in the itp file 
is your friend).

On 2012-02-22 10:41:34AM +0300, James Starlight wrote:
> Dear all :)
> 
> I have one extra question about Genion.
> 
> I want to neitralise my system with the qtot - 1.550002e by placing some Na
> and Cl ions under the physiological concetrantion 100 mmol/l
> 
> I've performed
> 
> genion -s ions.tpr -o b2ar_ions.gro -p topol.top -pname NA -nname CL -conc
> 0.1 -neutral
> 
> but insytead I've obtained system with 4.499977e-01 changre
> 
> What should I do to fix this problem?
> 
> James
> 
> 2012/2/16 Kathleen Kirchner 
> 
> > Dear James,
> >
> > I was working for a longer time on ion placement within more or less
> > equilibrated structures. I found my nearly magical miracle solving those
> > problems in not using any gromacs tool for producing the input structure
> > but rather use the free software Packmol:
> >
> > http://www.ime.unicamp.br/~**martinez/packmol/
> >
> > The software solves a mathematical minimization problem instead of putting
> > somewhere molecules and deleting others.
> >
> > After a short energy minimization of the obtained output structure (a few
> > 100 steps of steep algorithm) usally my systems work fine.
> >
> > Best
> > Kathleen
> >
> >
> > --
> > Kathleen Kirchner
> > PhD student
> > Max Planck Institute for Mathematics in the Sciences
> > (MPI f. Mathematik in den Naturwissenschaften)
> > Inselstr. 22-26, D04103 Leipzig
> > e-mail: kirch...@mis.mpg.de
> > web: 
> > http://www.mis.mpg.de/scicomp/**CompPhysChem/
> > Tel +49 341 9959 725
> > Fax +49 341 9959 999
> >
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/**
> > Support/Mailing_Lists/Searchbefore
> >  posting!
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> >

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-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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