Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

[Justin A. Lemkul]

On 5/7/12 1:01 AM, Anirban Ghosh wrote:



On Mon, May 7, 2012 at 10:17 AM, Bala S mailto:think_bey...@aol.com>> wrote:

Justin and Anirban,

I have another query on membrane simulation following your tutorials.

How do I insert only a part of protein into the lipid bilayer and carryout
the simulation?


editconf with -box option helps you to orient your protein with respect to the
bilayer. And visually in VMD you have the option of move a "molecule" under
"mouse" option in which you can move your protein wrt the bilayer (when the
bilayer and the protein .gro/.pdb files are loaded separately in VMD).



I have always found the VMD method to be hit-or-miss and often frustrating.  It 
is also possible to use the -center option of editconf to position the protein 
of interest at a given location, and/or use -translate or -rotate.


-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] Re: GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

On Mon, May 7, 2012 at 10:17 AM, Bala S  wrote:

> Justin and Anirban,
>
> I have another query on membrane simulation following your tutorials.
>
> How do I insert only a part of protein into the lipid bilayer and carryout
> the simulation?
>

editconf with -box option helps you to orient your protein with respect to
the bilayer. And visually in VMD you have the option of move a "molecule"
under "mouse" option in which you can move your protein wrt the bilayer
(when the bilayer and the protein .gro/.pdb files are loaded separately in
VMD).

-Anirban


>
> Thanks
> Bala S
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4957017.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

On Fri, Apr 27, 2012 at 7:37 PM, Justin A. Lemkul  wrote:

>
>
> On 4/27/12 10:00 AM, Bala S wrote:
>
>> Anirban,
>>
>> Exactly.. That's the gap (either side of the leaflets) I was mentioning
>> about. I'll try EM and check itagain.
>>
>>
> EM won't fill in solvent gaps.  If you're using my protocol for increasing
> the C radius in vdwradii.dat, then a small gap is normal and will close
> when doing equilibration as the solvent fills in around the lipid
> headgroups.
>
>  Yes, as Justin mentioned, the equilibration runs (restraining the
protein) will fill those gaps.

Anirban

-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] Re: GPCR MD Tutorial Using GROMACS (URL)

[Justin A. Lemkul]

On 4/27/12 10:00 AM, Bala S wrote:

Anirban,

Exactly.. That's the gap (either side of the leaflets) I was mentioning
about. I'll try EM and check itagain.



EM won't fill in solvent gaps.  If you're using my protocol for increasing the C 
radius in vdwradii.dat, then a small gap is normal and will close when doing 
equilibration as the solvent fills in around the lipid headgroups.


-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] Re: GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

On Fri, Apr 27, 2012 at 7:00 PM, Bala S  wrote:

> Anirban,
>
> Thank you. You guys are doing miracles with the biomolecules and solving
> almost all of my problems.
>
> I have followed your suggestion and could see now some more SOL molecules
> by
> increasing the z value.
>
> But I am seeing a substantial gap between the surface of the lipid bilayer
> and added SOL molecules in the visualizer. Is it normal or I have to do
> something about it?
>
>
I didn't really get your point. From the surface means on either side of
the leaflets? Or one thing you can do is to carry out the EM, and
equilibration runs (NVT and NPT) (restraining the protein) and see how the
waters orient them with respect to the bilayer.

Anirban


> Thanks
> Bala S
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933923.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

On Fri, Apr 27, 2012 at 6:31 PM, Bala S  wrote:

> Justin,
>
> OOPS!!
> Sorry for that.. Now I could realize it.
> Following up.. I have done further iterations with inflategro and reached
> 0.62 nm^2 which similar to what you have explained in the tutorial.
>
> Now, I could see the lipid bilayer really shrinked and no SOL molecules are
> seen in between. Now the issue I would like to have clarification on is
> that
> only 163 SOL molecules were added up and down which looks very scarce for
> the simulation.
>
> What is the solution?
>
>
First visualize and see whether the hydrophilic ends of the lipid bilayer
and your protein's part on either side of the bilayer (like a GPCR's intra
and extra cellular ends) are well immersed in the water box. If not, you
can increase the solvation box along the z-axis by increasing the z value
for -box option in editconf (keeping x and y values same).

Anirban


> Bala S
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933854.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

[Justin A. Lemkul]

On 4/27/12 8:38 AM, Bala S wrote:

Thanks Justin and Anirban for taking this long in TM simulations.

I'm following Justin's tutorial majorly and taking some clues from Anirban's
too when I need further clarification.


From both of your guidelines I could understand wht I should be doing before

solvating the system. Now, I have a question that how many iterations I
should perform with inflateGRO program and what is the basis to stop and
move with solvation step?

Justin's one says that he could reach ~72 Å2 (which is above the expt. value
~62Å2). But when I am exactly following the tutorial with same KALP peptide.
I am ending up with 'Area per lipid: 3.73355898918962 nm^2' within 10
iterations which is far lower than Justin's. Why?



3.73 nm^2 is 373 A^2 - mind the fact that the units have a square term.

-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] Re: GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

On Fri, Apr 27, 2012 at 4:59 PM, Justin A. Lemkul  wrote:

>
>
> On 4/27/12 6:40 AM, Bala S wrote:
>
>> Thanks for the reply.
>>
>> I'm following the tutorial.
>>
>>
> Please clarify whether you're using Anirban's or mine.  Now that two
> exist, people will have to be a fair bit more specific :)
>
>
>  In your system, to solvate it you have the values that was used during the
>> protien insertion into the bilayer. Following it, I have used the
>> following
>> commandfor my system where the protein is very much smaller than the
>> length
>> of the bilayer.
>>
>> $ editconf -f shrinked4.gro -o shrinked4_1.gro -box 6.41840 6.44350
>> 6.59650
>>
>> $ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top
>>
>>
> If you have to manipulate the box of any coordinate file produced by
> InflateGRO, whatever you're doing is wrong.  You should not be solvating
> anything until the very last step of the procedure, where your bilayer is
> of correct size and APL.


Exactly, solvate at the end of all the compression steps performed by
InflateGro (may be 10 or 20 depending on your system) and minimizations (of
only protein + lipid)  until you have reached the correct area per lipid.
And then only solvate. Check for the dimensions in the last line of the
FINAL (compressed and minimized) .gro file and then solvate

Thanks,

Anirban

>
>
>  But I could see in the visualizer that SOL molecules were added on top and
>> bottom but only 1/3 of the length of the bilayer.
>> How to add SOL molecules to whole length or how to remove not-solvated
>> part
>> of lipids?
>>
>>
> This outcome is a consequence of re-adjusting the box size of a system
> that likely has other dimensions.  As far as I can tell, you shouldn't be
> doing this.
>
>
> -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] Re: GPCR MD Tutorial Using GROMACS (URL)

[Justin A. Lemkul]

On 4/27/12 6:40 AM, Bala S wrote:

Thanks for the reply.

I'm following the tutorial.



Please clarify whether you're using Anirban's or mine.  Now that two exist, 
people will have to be a fair bit more specific :)



In your system, to solvate it you have the values that was used during the
protien insertion into the bilayer. Following it, I have used the following
commandfor my system where the protein is very much smaller than the length
of the bilayer.

$ editconf -f shrinked4.gro -o shrinked4_1.gro -box 6.41840 6.44350 6.59650

$ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top



If you have to manipulate the box of any coordinate file produced by InflateGRO, 
whatever you're doing is wrong.  You should not be solvating anything until the 
very last step of the procedure, where your bilayer is of correct size and APL.



But I could see in the visualizer that SOL molecules were added on top and
bottom but only 1/3 of the length of the bilayer.
How to add SOL molecules to whole length or how to remove not-solvated part
of lipids?



This outcome is a consequence of re-adjusting the box size of a system that 
likely has other dimensions.  As far as I can tell, you shouldn't be doing this.


-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] Re: GPCR MD Tutorial Using GROMACS (URL)

[Justin A. Lemkul]

On 4/27/12 6:04 AM, Anirban Ghosh wrote:



On Fri, Apr 27, 2012 at 3:27 PM, Bala S mailto:think_bey...@aol.com>> wrote:

Thank you for that clarification.

I found that there were SOL molecules in .top file. I could run the EM now.

Coming to the Solvation step, I'm facing a problem.

I have made the mentioned change (0.15 to 0.375 for C) in the vdwradii.dat
locally.

While adding the solvent molecules, what command should I be using?

I am using the usual command I use for non-membrane simulations,

$ editconf -f shrinked4.gro -o shrinked4_1.gro -c -d 1 -bt cubic

followed by

$ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top


When you mention -bt cubic, it adds a cubic water box all around your system (if
you visualize you will see your entire bilayer immersed in a cubic water box
like a normal protein solvation). But that is wrong. You need to add water only
on either side of the lipid membrane (that is along the z-axis only). So use the
-box option with editconf without using -c and -d. You can have a look at
https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial It is clearly
mentioned over there how to go about it.




You should not add water in between InflateGRO steps.  The process should be 
carried out entirely in the absence of water, otherwise you add solvent to a 
huge box and the water is incorporated into the voids in the lipid membrane. 
Only after the last shrinking step should you proceed with adding water.


-Justin


calculation goes for long time showing a huge number of SOL molecules.

I guess I'm worng somehere.

Thanks.

Bala S





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--


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] Re: GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

On Fri, Apr 27, 2012 at 3:27 PM, Bala S  wrote:

> Thank you for that clarification.
>
> I found that there were SOL molecules in .top file. I could run the EM now.
>
> Coming to the Solvation step, I'm facing a problem.
>
> I have made the mentioned change (0.15 to 0.375 for C) in the vdwradii.dat
> locally.
>
> While adding the solvent molecules, what command should I be using?
>
> I am using the usual command I use for non-membrane simulations,
>
> $ editconf -f shrinked4.gro -o shrinked4_1.gro -c -d 1 -bt cubic
>
> followed by
>
> $ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top
>

When you mention -bt cubic, it adds a cubic water box all around your
system (if you visualize you will see your entire bilayer immersed in a
cubic water box like a normal protein solvation). But that is wrong. You
need to add water only on either side of the lipid membrane (that is along
the z-axis only). So use the -box option with editconf without using -c and
-d. You can have a look at
https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial It is clearly
mentioned over there how to go about it.


>
> calculation goes for long time showing a huge number of SOL molecules.
>
> I guess I'm worng somehere.
>
> Thanks.
>
> Bala S
>
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933479.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

On Fri, Apr 27, 2012 at 1:01 PM, Bala S  wrote:

> Dear Justin
>
> Thanks for the explanation.
>
> I am following your tutorial of KALP membrane simulation. I am stuck in
> between two steps of InflateGRO. After the first step, the tutorial
> requests
> to perform EM. Should I be running grompp with new system_inflated.gro file
> to generate a new .tpr file for EM or should I perform EM with em.tpr
> which

was generated some time back in the tutorial?


You should run grompp with the inflated .gro file (system_inflated.gro)
since you will be minimizing the inflated .gro file after every compression
step to remove bad contacts. The earlier em.tpr was used to remove
periodicity of the bilayer only.


> The latter ran EM but the
> former shows error 'number of coordinates in coordinate file
> (system_inflated.gro, 6438)
> does not match topology (topol.top, 17403)"
>

The difference in atom numbers might be because your .top file contains
some extra molecules in the [ molecules ] section (may be SOL). Use .top
file that contains only protein and lipid molecules.


> Thanks.
>
> Bala S
>
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933137.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

Hello Bala,

Yes, exactly as Justin said it represents just a workflow where a GPCR
protein (here B2AR) has been taken as an example. I mentioned it as a GPCR
tutorial because many often inquire about GPCR MD simulations only in the
forum. But it can be adapted for other membrane proteins as well. And
secondly again as Justin mentioned, the choice of lipid depends upon the
system you wish to replicate.

Regards,

Anirban

On Thu, Apr 26, 2012 at 11:10 PM, Justin A. Lemkul  wrote:

>
>
> On 4/26/12 9:35 AM, Bala S wrote:
>
>> Dear Anirban,
>>
>> Thanks for the tutorial you have created for the newbies like me to
>> follow.
>>
>> I wonder the tutorial is only for the GPCRs not applicable for other
>> membrane proteins?
>>
>>
> Tutorials present possible workflows.  Anirban's tutorial does not
> significantly differ from my own (linked from his) which I happen to know
> has been applied to many different systems.  There is nothing GPCR-specific
> in this new tutorial, just like there is nothing KALP-specific about mine.
>
>
>  I also have another question about slecting a lipidbilayer, what is the
>> criteria is selecting it, for instance popc, dopc or dppc?
>>
>>
> The choice of lipid depends on what you need to model.
>
> -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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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

[Peter C. Lai]

Looks I got to the party late (at a conference with limited time to do emails).

As a shameless self-plug, we recently published a soup-to-nuts protocol paper
for GPCR + POPC + ligand in Gromacs 4.5.x and CHARMM27/36/CGenFF.

Our timescales are on the order 100+ns.

20ns/day is possible on 100K atoms with around 200 xeon x5650 cores over
qdr infiniband (4-order PME with 1.2nm cutoffs 0.16 fourier spacing, vdwtype 
switch=0.8 and h-bond LINCS with 0.002ps dt).

http://www.frontiersin.org/Bioinformatics_and_Computational_Biology/10.3389/fgene.2012.00061/abstract

On 2012-04-26 01:40:17PM -0400, Justin A. Lemkul wrote:
> 
> 
> On 4/26/12 9:35 AM, Bala S wrote:
> > Dear Anirban,
> >
> > Thanks for the tutorial you have created for the newbies like me to follow.
> >
> > I wonder the tutorial is only for the GPCRs not applicable for other
> > membrane proteins?
> >
> 
> Tutorials present possible workflows.  Anirban's tutorial does not 
> significantly 
> differ from my own (linked from his) which I happen to know has been applied 
> to 
> many different systems.  There is nothing GPCR-specific in this new tutorial, 
> just like there is nothing KALP-specific about mine.
> 
> > I also have another question about slecting a lipidbilayer, what is the
> > criteria is selecting it, for instance popc, dopc or dppc?
> >
> 
> The choice of lipid depends on what you need to model.
> 
> -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
> 
> 
> -- 
> 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/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
==
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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Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

[Justin A. Lemkul]

On 4/26/12 9:35 AM, Bala S wrote:

Dear Anirban,

Thanks for the tutorial you have created for the newbies like me to follow.

I wonder the tutorial is only for the GPCRs not applicable for other
membrane proteins?



Tutorials present possible workflows.  Anirban's tutorial does not significantly 
differ from my own (linked from his) which I happen to know has been applied to 
many different systems.  There is nothing GPCR-specific in this new tutorial, 
just like there is nothing KALP-specific about mine.



I also have another question about slecting a lipidbilayer, what is the
criteria is selecting it, for instance popc, dopc or dppc?



The choice of lipid depends on what you need to model.

-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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