[gmx-users] Joining peptide chains using Gromacs

Grace Mugumbate mgmgra001 at uct.ac.za
Wed Aug 22 09:26:34 CEST 2007


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

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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 <leehk at umich.edu>
Subject: [gmx-users] How to make grids in lipid bilayer (to measure
	contour	length)
To: gmx-users at gromacs.org
Message-ID: <20070822001610.jcw30yfggw44c8w8 at web.mail.umich.edu>
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 " <sp1020 at gmail.com>
Subject: Re: [gmx-users] Ionic liquids
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
	<bd5475eb0708212133v6b44b48awfa71fc1e536284d at mail.gmail.com>
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 <sampo.karkola at helsinki.fi> 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
> sampo.karkola at helsinki.fi
>
> SeungPyo Hong wrote:
> >
> > On 8/16/07, *Mark Abraham* <Mark.Abraham at anu.edu.au
> > <mailto:Mark.Abraham at anu.edu.au>> 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 at gromacs.org
> >     <mailto:gmx-users at 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 gmx-users-request at gromacs.org
> >     <mailto:gmx-users-request at gromacs.org>.
> >     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
> > sphong_ at kaist.ac.kr <mailto:sphong_ at kaist.ac.kr>
> > sp1020 at gmail.com <mailto:sp1020 at gmail.com>
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>



-- 
--------------------------------------------------
'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
sphong_ at kaist.ac.kr
sp1020 at gmail.com
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------------------------------

Message: 3
Date: Wed, 22 Aug 2007 08:38:47 +0300
From: Sampo Karkola <sampo.karkola at helsinki.fi>
Subject: Re: [gmx-users] Ionic liquids
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <46CBCBE7.8080504 at helsinki.fi>
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
sampo.karkola at helsinki.fi

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* <sampo.karkola at helsinki.fi 
> <mailto:sampo.karkola at helsinki.fi>> 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
>     sampo.karkola at helsinki.fi <mailto:sampo.karkola at helsinki.fi>
> 
>     SeungPyo Hong wrote:
>      >
>      > On 8/16/07, *Mark Abraham* < Mark.Abraham at anu.edu.au
>     <mailto:Mark.Abraham at anu.edu.au>
>      > <mailto:Mark.Abraham at anu.edu.au
>     <mailto:Mark.Abraham at anu.edu.au>>> 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 at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>      >     <mailto:gmx-users at gromacs.org <mailto:gmx-users at 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 gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>
>      >     <mailto:gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>>.
>      >     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
>      > sphong_ at kaist.ac.kr <mailto:sphong_ at kaist.ac.kr>
>     <mailto:sphong_ at kaist.ac.kr <mailto:sphong_ at kaist.ac.kr>>
>      > sp1020 at gmail.com <mailto:sp1020 at gmail.com>
>     <mailto:sp1020 at gmail.com <mailto:sp1020 at gmail.com>>
>      >
>      >
>      >
>     ------------------------------------------------------------------------
>      >
>      > _______________________________________________
>      > gmx-users mailing list     gmx-users at gromacs.org
>     <mailto:gmx-users at 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 gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>      > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>     _______________________________________________
>     gmx-users mailing list     gmx-users at gromacs.org
>     <mailto:gmx-users at 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 gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     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
> sphong_ at kaist.ac.kr <mailto:sphong_ at kaist.ac.kr>
> sp1020 at gmail.com <mailto:sp1020 at gmail.com>
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


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