Dear Gromacs Users,
I am building a G-protein coupled receptor molecule. I have used homology
modelling to build the seven helices and Molecular dynamics with Gromacs to
build the loops. I then converted the .gro files to .pdb files using trjconv.
Now I would like to join the loops to the helices, is there a way of doing that
with Gromacs?
Thank you for your help?
Grace
PhD student
>>> <[EMAIL PROTECTED]> 08/22/07 7:40 AM >>>
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Today's Topics:
1. How to make grids in lipid bilayer (to measure contour
length) (Hwankyu Lee)
2. Re: Ionic liquids (SeungPyo Hong )
3. Re: Ionic liquids (Sampo Karkola)
----------------------------------------------------------------------
Message: 1
Date: Wed, 22 Aug 2007 00:16:10 -0400
From: Hwankyu Lee <[EMAIL PROTECTED]>
Subject: [gmx-users] How to make grids in lipid bilayer (to measure
contour length)
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format="flowed"
Dear gmx-users,
I'm trying to calculate contour length of huge lipid bilayer with
undulation (non-projected area per lipid). In order to calculate that
accurately, I would like to measure contour length in local areas of
bilayer by making lots of grids in lipid bilayer. I'm wondering if
there is a tool or way to make grids in lipid bilayer in the .xtc
trajectories.
Thank you for your help in advance.
best,
Hwankyu.
------------------------------
Message: 2
Date: Wed, 22 Aug 2007 13:33:00 +0900
From: "SeungPyo Hong " <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Ionic liquids
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Sorry for late respond~
I totally agree with you.
Frankly, I don't have any idea about that kind of idea.
I just help the guy to do what he want to do.
Anyhow, as Mark said, I think some experiment is required to get a
meaningful result.
First I warn you that this is not a good approach at all.
He want to simulate [EtNH3]+ [NO3]-.
I think that the structure of the is relatively simple and thus made their
structure with WebMO(Gaussian).
Then to get the groamcs topology, I use PRODRG server.
The partial charge of them are corrected to same as Gaussian result.
Then I placed them in a lattice with a same interval.
And run MD simulation with only solvent.
By doing this I can get a solvent coordinate in a box.
Using this solvent coordinate and topology, you can run MD.
But PRODRG does not give an accurate information and thus be careful.
Good luck
On 8/16/07, Sampo Karkola <[EMAIL PROTECTED]> wrote:
>
> Hi,
>
> nice to hear that someone else is also interested in doing MD in room
> temperature ionic liquids. What kind of ions do you use? Bmim chlorides
> perhaps, or do you have a larger counterion to bmim? Or a completely
> different cation? As Mark pointed out, if you do not have a properly
> parameterised force field for ILs, the results probably are not
> reliable, but I still would like to hear how did you define the
> parameters and how the mdruns performed.
>
> Regards,
>
> Sampo
>
> ______________________________
> Sampo Karkola
> Doctoral student
>
> Laboratory of Organic Chemistry
> Department of Chemistry
> POBox 55, FIN-00014
> University of Helsinki
> Finland
>
> tel. +358 9 19150369
> fax. +358 9 19150366
> [EMAIL PROTECTED]
>
> SeungPyo Hong wrote:
> >
> > On 8/16/07, *Mark Abraham* <[EMAIL PROTECTED]
> > <mailto:[EMAIL PROTECTED]>> wrote:
> >
> > Sampo Karkola wrote:
> > > Dear all,
> > >
> > > I was wondering if there are any parameters defined for ionic
> > liquids?
> > > Some enzymes have retained their activity when the solvent has
> been a
> > > mixture of water and ionic liquids and it would be interesting to
> > study
> > > the actual catalytical reactions in such a solvent.
> >
> > I don't know how you can mix an ionic liquid and water and not get a
> > really hot aqueous solution that would smash an enzyme :-)
> >
> > > I'm not an expert on the ionic liquids field or in simulating
> > reactions,
> > > but ionic liquids have been used in eg. microwave-assisted
> synthesis
> > > with promising results. If one wants to study the reactions that
> take
> > > place in ionic liquids, with or without an enzyme catalysing it,
> are
> > > there any well-known procedures to follow? Is Gromacs the correct
> > tool
> > > for that? I'm not going to study such reactions, at least not at
> the
> > > moment, but I'd just like to know how/if they can be done.
> >
> > If you distort the solvent too far from pure water, the
> parameterization
> > process of these force fields will no longer be valid for studying
> the
> > systems you want. Parameterizing new force fields for these solvents
> is
> > probably not a worthwhile undertaking, and definitely not one to do
> > lightly.
> >
> > Mark
> > _______________________________________________
> > gmx-users mailing list gmx-users@gromacs.org
> > <mailto:gmx-users@gromacs.org>
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search
> > <http://www.gromacs.org/search> before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to [EMAIL PROTECTED]
> > <mailto:[EMAIL PROTECTED]>.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > What a coincidence!
> > A student in the biology major come to me he want to do simulation with
> > ionic liquid.
> > I have much doubt about that kind of simulation but becase he is eager
> > to do it.
> > I try to make the solvent by placing the molecules in lattice and run MD
> > under pressure coupling.
> > Though I am also a beginner in this field, I am not sure of the
> > plausiblity of this method but it seems to be OK to me.
> >
> > --
> > --------------------------------------------------
> > 'God used beautiful mathematics in creating the world.'
> > -Paul Dirac
> > 'But he created too many object.'
> > -Seungpyo Hong
> >
> > Seungpyo Hong
> > Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon
> Korea
> > Tel. (82)-18-372-2468
> > [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
> > [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to [EMAIL PROTECTED]
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
--------------------------------------------------
'God used beautiful mathematics in creating the world.'
-Paul Dirac
'But he created too many objects.'
-Seungpyo Hong
Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
[EMAIL PROTECTED]
[EMAIL PROTECTED]
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------------------------------
Message: 3
Date: Wed, 22 Aug 2007 08:38:47 +0300
From: Sampo Karkola <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Ionic liquids
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi and thanks for sharing,
as pointed out earlier in this list, there is a published force field
for ILs to be used in gromacs. Maybe that would be a good starting point
for you, too. If I remember correct, they did not have the same ions,
but they had the most common ones.
I am not going to do any simulations with ILs, I'm just curious to see
the development around ILs.
Regards,
Sampo
______________________________
Sampo Karkola
Doctoral student
Laboratory of Organic Chemistry
Department of Chemistry
POBox 55, FIN-00014
University of Helsinki
Finland
tel. +358 9 19150369
fax. +358 9 19150366
[EMAIL PROTECTED]
SeungPyo Hong wrote:
> Sorry for late respond~
> I totally agree with you.
> Frankly, I don't have any idea about that kind of idea.
> I just help the guy to do what he want to do.
> Anyhow, as Mark said, I think some experiment is required to get a
> meaningful result.
>
> First I warn you that this is not a good approach at all.
> He want to simulate [EtNH3]+ [NO3]-.
> I think that the structure of the is relatively simple and thus made
> their structure with WebMO(Gaussian).
> Then to get the groamcs topology, I use PRODRG server.
> The partial charge of them are corrected to same as Gaussian result.
>
> Then I placed them in a lattice with a same interval.
> And run MD simulation with only solvent.
> By doing this I can get a solvent coordinate in a box.
>
> Using this solvent coordinate and topology, you can run MD.
> But PRODRG does not give an accurate information and thus be careful.
>
> Good luck
>
> On 8/16/07, *Sampo Karkola* <[EMAIL PROTECTED]
> <mailto:[EMAIL PROTECTED]>> wrote:
>
> Hi,
>
> nice to hear that someone else is also interested in doing MD in room
> temperature ionic liquids. What kind of ions do you use? Bmim chlorides
> perhaps, or do you have a larger counterion to bmim? Or a completely
> different cation? As Mark pointed out, if you do not have a properly
> parameterised force field for ILs, the results probably are not
> reliable, but I still would like to hear how did you define the
> parameters and how the mdruns performed.
>
> Regards,
>
> Sampo
>
> ______________________________
> Sampo Karkola
> Doctoral student
>
> Laboratory of Organic Chemistry
> Department of Chemistry
> POBox 55, FIN-00014
> University of Helsinki
> Finland
>
> tel. +358 9 19150369
> fax. +358 9 19150366
> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
>
> SeungPyo Hong wrote:
> >
> > On 8/16/07, *Mark Abraham* < [EMAIL PROTECTED]
> <mailto:[EMAIL PROTECTED]>
> > <mailto:[EMAIL PROTECTED]
> <mailto:[EMAIL PROTECTED]>>> wrote:
> >
> > Sampo Karkola wrote:
> > > Dear all,
> > >
> > > I was wondering if there are any parameters defined for ionic
> > liquids?
> > > Some enzymes have retained their activity when the solvent
> has been a
> > > mixture of water and ionic liquids and it would be
> interesting to
> > study
> > > the actual catalytical reactions in such a solvent.
> >
> > I don't know how you can mix an ionic liquid and water and
> not get a
> > really hot aqueous solution that would smash an enzyme :-)
> >
> > > I'm not an expert on the ionic liquids field or in simulating
> > reactions,
> > > but ionic liquids have been used in eg. microwave-assisted
> synthesis
> > > with promising results. If one wants to study the
> reactions that take
> > > place in ionic liquids, with or without an enzyme
> catalysing it, are
> > > there any well-known procedures to follow? Is Gromacs the
> correct
> > tool
> > > for that? I'm not going to study such reactions, at least
> not at the
> > > moment, but I'd just like to know how/if they can be done.
> >
> > If you distort the solvent too far from pure water, the
> parameterization
> > process of these force fields will no longer be valid for
> studying the
> > systems you want. Parameterizing new force fields for these
> solvents is
> > probably not a worthwhile undertaking, and definitely not one
> to do
> > lightly.
> >
> > Mark
> > _______________________________________________
> > gmx-users mailing list gmx-users@gromacs.org
> <mailto:gmx-users@gromacs.org>
> > <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search
> > < http://www.gromacs.org/search> before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to [EMAIL PROTECTED]
> <mailto:[EMAIL PROTECTED]>
> > <mailto:[EMAIL PROTECTED]
> <mailto:[EMAIL PROTECTED]>>.
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> <http://www.gromacs.org/mailing_lists/users.php>
> >
> >
> > What a coincidence!
> > A student in the biology major come to me he want to do
> simulation with
> > ionic liquid.
> > I have much doubt about that kind of simulation but becase he is
> eager
> > to do it.
> > I try to make the solvent by placing the molecules in lattice and
> run MD
> > under pressure coupling.
> > Though I am also a beginner in this field, I am not sure of the
> > plausiblity of this method but it seems to be OK to me.
> >
> > --
> > --------------------------------------------------
> > 'God used beautiful mathematics in creating the world.'
> > -Paul Dirac
> > 'But he created too many object.'
> > -Seungpyo Hong
> >
> > Seungpyo Hong
> > Master student at PBIL(Protein BioInformatics Lab.) in KAIST,
> Daejeon Korea
> > Tel. (82)-18-372-2468
> > [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
> <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
> > [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
> <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
> >
> >
> >
> ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users@gromacs.org
> <mailto:gmx-users@gromacs.org>
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to [EMAIL PROTECTED]
> <mailto:[EMAIL PROTECTED]>.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> <mailto:gmx-users@gromacs.org>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
> <mailto:[EMAIL PROTECTED]>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> --
> --------------------------------------------------
> 'God used beautiful mathematics in creating the world.'
> -Paul Dirac
> 'But he created too many objects.'
> -Seungpyo Hong
>
> Seungpyo Hong
> Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
> Tel. (82)-18-372-2468
> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------
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