From owner-chemistry@ccl.net Fri Jun 29 07:35:00 2012 From: "Felipe Pineda pideca_-_hotmail.com" To: CCL Subject: CCL: Lipid membrane modeling tool (summary of responses) Message-Id: <-47156-120629045315-20801-tU4U4YUR734TGvaTKHH6Ng+/-server.ccl.net> X-Original-From: Felipe Pineda Content-Type: multipart/alternative; boundary="_934628b5-0277-4812-a8b1-043fbe7fd6b5_" Date: Fri, 29 Jun 2012 10:53:04 +0200 MIME-Version: 1.0 Sent to CCL by: Felipe Pineda [pideca() hotmail.com] --_934628b5-0277-4812-a8b1-043fbe7fd6b5_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 DQoNCg0KDQoNCg0KDQoNCg0KDQoNCg0KDQoNCg0KDQoNCg0KDQpEZWFyIENDTGVyczoNCg0KbW9y ZSB0aGFuIG9uZSBtb250aCBhZ28sIEkgcG9zdGVkIHRoZSBmb2xsb3dpbmcgcXVlcnkgKHNvbWV3 aGF0IG91dHNpZGUgdGhlIEdhdXNzaWFuIG1haW5zdHJlYW0pIHRvIENDTCBhbmQgcmVjZWl2ZWQg dGhlcmVhZnRlciBzZXZlcmFsIHJlc3BvbnNlcy4gQWZ0ZXIgSSBhbG1vc3QgZm9yZ290IGFib3V0 IGl0LCBJIHJlY2VpdmVkIHllc3RlcmRheSBvbmUgbW9yZSBjb250cmlidXRpb24sIHdoaWNoIHJl 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X-Original-From: "Nikolaos Bouropoulos" Date: Fri, 29 Jun 2012 11:28:14 -0400 Sent to CCL by: "Nikolaos Bouropoulos" [nbouro^^^upatras.gr] The upcoming journal Advanced Chemistry Letters invites authors to submit articles. Manuscripts must be prepared according to Journals guidelines, available at http://www.aspbs.com/acl/ Submit your manuscripts directly to Dr. N. Bouropoulos via editoracl*upatras.gr All papers submitted to this issue will be subject to a peer review process to ensure high quality articles. Submitted papers should not have been previously published nor be currently under consideration for publication elsewhere. -- Nikolaos Bouropoulos Assistant Professor Department of Materials Science University of Patras, GR-26504 Rio Patras, Greece Phone: (+030) 2610 997164, e-mail: nbouro*upatras.gr Editor-in-Chief: Advanced Chemistry Letters. http://www.aspbs.com/acl/ e-mail: editoracl*upatras.gr From owner-chemistry@ccl.net Fri Jun 29 15:00:00 2012 From: "John Keller jwkeller++alaska.edu" To: CCL Subject: CCL:G: Lipid membrane modeling tool (summary of responses) Message-Id: <-47158-120629120538-8380-0bBT1S5j/0UI39OvtaVgXQ*_*server.ccl.net> X-Original-From: John Keller Content-Type: multipart/alternative; boundary=20cf307f334291e9fb04c39e9d7b Date: Fri, 29 Jun 2012 08:05:20 -0800 Mime-Version: 1.0 (1.0) Sent to CCL by: John Keller [jwkeller__alaska.edu] --20cf307f334291e9fb04c39e9d7b Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable We have used the excellent Desmond package from www.DEShawRsearch.com. It's free for academia. John Keller University of Alaska Fairbanks Sent from my iPad On Jun 29, 2012, at 4:41 AM, "Felipe Pineda pideca_-_hotmail.com" < owner-chemistry]=[ccl.net> wrote: Dear CCLers: more than one month ago, I posted the following query (somewhat outside the Gaussian mainstream) to CCL and received thereafter several responses. After I almost forgot about it, I received yesterday one more contribution, which reminded me on duly acknowledging the kind contributions and summarize the answers, which used to be a good practice in CCL in the past. Here they are for whomever they could matter: *Original query* > From: owner-chemistry]=[ccl.net > To: fpineda]=[uni-bonn.de > Subject: CCL: Lipid membrane modeling tool > Date: Sun, *20 May 2012* 09:37:09 -0400 > > > Sent to CCL by: "Felipe Pineda" [pideca:+:hotmail.com] > Dear CCLers! > > *I'd greatly appreciate any pointer to state-of-the-art, non-commercial molecular modeling tools for mono- and bilayer lipid membranes. I searched the CCL archive, but couldn't find any useful information. * Response #1 by *Richard Wood*: Date: Sun, 20 May 2012 12:17:46 -0500 > From: rwoodphd]=[msn.com To: fpineda]=[uni-bonn.de Subject: Re: CCL: [CCL] Lipid membrane modeling tool *I'd try the CHARMM GUI web site for starters.* http://www.charmm-gui.org/ Richard Response #2 by *Richard Venable*: > From: owner-chemistry]=[ccl.net > To: fpineda]=[uni-bonn.de > Subject: CCL: [CCL] Lipid membrane modeling tool > Date: Sun, 20 May 2012 14:13:40 -0400 > > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler * nhlbi.nih.gov] *> For building bilayer models with CHARMM FF suitable for use with CHARMM or > NAMD, I suggest > > www.charmm-gui.org > > In CHARMM, converting a bilayer model into a symmetric dual leaflet > monolayer system is fairly easy; a thicker water layer is strongly advised.* > > -- > Rick Venable 5635 FL/T906 Response #3 by *Andreas Klamt*: > From: owner-chemistry]=[ccl.net > To: fpineda]=[uni-bonn.de > Subject: CCL: Lipid membrane modeling tool > Date: Sun, 20 May 2012 19:01:42 +0200 > > > Sent to CCL by: Andreas Klamt [klamt^cosmologic.de] > Hi Felipe, > *> we do have the COSMOmic extension of COSMotherm, which calculates the > distribution of molecules in micellar systems, incl. biomembranes. > See: COSMOmic: A Mechanistic Approach to the Calculation of > Membrane=E2=88=92Water Partition Coefficients and Internal Distributions = within > Membranes and Micelles > by: Andreas Klamt, Uwe Huniar, Simon Spycher, Jo=CC=88rg Keldenich > The Journal of Physical Chemistry B, Vol. 112, No. 38. (25 September > 2008), pp. 12148-12157, doi:10.1021/jp801736k > But it is not free, though our academic prices are quite moderate.* > > Best regards > > Andreas Response #4 by *Siegfried Hoefinger*: > From: siegfried.hoefinger]=[unibo.it > To: pideca]=[hotmail.com > Subject: re: CCL: Lipid membrane modeling tool > Date: Mon, 21 May 2012 07:25:19 +0000 > > > Hi Felipe, > *> For proteins, maybe the following can already provide some clues.. > > http://84.113.253.84/~polch > --> Jobs, Submit a job (pdb file) > --> Select your seolvent/environment, Membrane Mimicry* > > all the best > sig Response #5 by *Pablo Englebienne*: > From: owner-chemistry]=[ccl.net > To: fpineda]=[uni-bonn.de > Subject: CCL: Lipid membrane modeling tool > Date: Thu, 28 Jun 2012 11:27:59 +0200 > > > Sent to CCL by: Pablo Englebienne [p.englebienne : tue.nl] *> Hi Felipe, I'm not sure specifically what you are trying to accomplish > with respect to the lipid membranes, but if what you're looking after is > atomistic MD simulations involving a lipid bilayer and perhaps some > solutes, Gromacs may be able to handle it. > > I found the tutorials written by Justin Lemkul quite instructive as a > starting point: > http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.ht= ml > > Tutorial #2 deals specifically with building a lipid membrane with a > peptide solute. > > Regards, > Pablo* Many thanks to both Richards, to Andreas, Siegfried, and last but not least to Pablo for their replies. I have first to say that I am indeed interested in carrying out atomistic, classical MD simulations (with GROMACS) on models of archeal membranes. These membranes differ from eukaryotik ones in their composition. They consist of bipolar tetraether, macrocyclic, so called bola lipids, forming monolayers instead of conventional, di-ester lipids forming bilayers in the latter. And this is the main issue. I tried CHARMM GUI, which is really a very useful tool for building membrane models, but "only" 30 "standard" (diester, or diacylglycerids) lipids are available for membrane model building in its library. I asked the developers and got the following feedback from Sunhwan Jo (thanks a lot to him too): *> 1. Is it possible to build a homogeneous lipid bilayer? The corresponding selection seems to not be active* Yes, just use the lipid composition input box, and put 1 as the ratio of the lipid type that you would like to build. >* 2. Is it possible to use my own lipids (not conventional di-ester, but di- or tetraether lipids) by supplying the corresponding PDB fle? Only "conventional" (phospho)lipids are listed* No, right now, we don't have a method to include custom lipid into the building process. However, you can build the bilayer with a lipid type, and use the input files generated by the Membrane Builder as a example to include your lipid. I'm currently trying to do the latter, but it's tough. Another tool, *PACKM= OL *, was also recommended to me. I haven't tried it yet. Regarding the GROMACS tutorial recommended by Pablo: here a ready DPPC-membrane model ("dppc128.pdb - the structure of a 128-lipid DPPC bilayer" ) is used. My current goal is to build a similar, but monolayer model, with my own lipid since I don't get it off the shelf. I would have then to hydrate it and add alkali and halide ions to it. Lots to do ... Thank you again for all the helpful contributions and best regards, Felipe --20cf307f334291e9fb04c39e9d7b Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
We have used the excellen= t Desmond package from www.DEShawR= search.com. It's free for academia.
John Keller
University of Alaska Fairbanks


Sent from my iPad

On Jun 29, 2012, at 4:41 AM, "Felipe Pineda pideca_-_hotmail.com" <owner-chemistry]=[ccl.net> wrote:

Dear CCLers:

more than one month ago, I posted the = following query (somewhat outside the Gaussian mainstream) to CCL and recei= ved thereafter several responses. After I almost forgot about it, I receive= d yesterday one more contribution, which reminded me on duly acknowledging = the kind contributions and summarize the answers, which used to be a good p= ractice in CCL in the past. Here they are for whomever they could matter:
Original query

> From: owner-chemistry]=[ccl.net
> To: fpineda]=[uni-bonn.de
> Subject: CCL: Lipid membran= e modeling tool
> Date: Sun, 20 May 2012 09:37:09 -0400
>
>
>= Sent to CCL by: "Felipe Pineda" [pideca:+:hotmail.com]
> Dear CCLers!
>
> I'd greatly appreciate any pointer to state-of-the-art, non-commerc= ial=20 molecular modeling tools for mono- and bilayer lipid membranes. I=20 searched the CCL archive, but couldn't find any useful information.

Response #1 by Richard Wood:

Date: Sun, 20 May 2012 = 12:17:46 -0500
From: rwoodphd]=[msn.co= m
To: fpineda]=[uni-bonn.de
Subje= ct: Re: CCL: [CCL] Lipid membrane modeling tool

I'd try the CHARMM GUI web site for starters.
=C2=A0
=C2=A0
Richard

Response #2 by Richard Venable:

> Fr= om: owner-chemistry]=[ccl.net<= br>> To: fpineda]=[uni-bonn.de<= br> > Subject: CCL: [CCL] Lipid membrane modeling tool
> Date: Sun, 20= May 2012 14:13:40 -0400
>
>
> Sent to CCL by: "Ve= nable, Richard (NIH/NHLBI) [E]" [venabler * nhlbi.nih.gov]
> For building bilayer models with CHARMM FF suitable for use with CH= ARMM or
> NAMD, I suggest
>
> www.charmm-gui.org
>
> In CHARMM, converting= a bilayer model into a symmetric dual leaflet
> monolayer system is fairly easy; a thicker water layer is strongly adv= ised.
>
> --
> Rick Venable 5635 FL/T906
Response #3 by Andreas Klamt:

> From: owner-chemistry]=[ccl.net
> To: fpineda]=[uni-bonn.de
= > Subject: CCL: Lipid membrane modeling tool
> Date: Sun, 20 May 2= 012 19:01:42 +0200
>
>
> Sent to CCL by: Andreas Klamt = [klamt^cosmologic.de]
> Hi Felipe,
>
> we do have the COSMOmic extension of CO= SMotherm, which calculates the
> distribution of molecules in micell= ar systems, incl. biomembranes.
> See: COSMOmic: A Mechanistic Approa= ch to the Calculation of
> Membrane=E2=88=92Water Partition Coefficients and Internal Distributio= ns within
> Membranes and Micelles
> by: Andreas Klamt, Uwe Hu= niar, Simon Spycher, Jo=CC=88rg Keldenich
> The Journal of Physical C= hemistry B, Vol. 112, No. 38. (25 September
> 2008), pp. 12148-12157, doi:10.1021/jp801736k
> But it is not fr= ee, though our academic prices are quite moderate.
>
> Bes= t regards
>
> Andreas

Response #4 by Siegfried Hoefi= nger:

> From: siegfried.ho= efinger]=[unibo.it
> To: pide= ca]=[hotmail.com
> Subject: re: CCL: Lipid membrane modeling tool <= br> > Date: Mon, 21 May 2012 07:25:19 +0000
>
>
> Hi Fel= ipe,
>
> For proteins, maybe the following can already prov= ide some clues..
>
> h= ttp://84.113.253.84/~polch
> --> Jobs, Submit a job (pdb file)
> --> Se= lect your seolvent/environment, Membrane Mimicry
>
> all t= he best
> sig

Response #5 by Pablo Englebienne:

> From: owner-chemistry]=[c= cl.net
> To: fpineda]=[uni-b= onn.de
> Subject: CCL: Lipid membrane modeling tool
> Date:= Thu, 28 Jun 2012 11:27:59 +0200
>
>
> Sent to CCL by: Pablo Englebienne [p.englebienne : <= a href=3D"http://tue.nl">tue.nl]
> Hi Felipe, I'm not sure= specifically what you are trying to accomplish
> with respect to th= e lipid membranes, but if what you're looking after is
> atomistic MD simulations involving a lipid bilayer and perhaps some > solutes, Gromacs may be able to handle it.
>
> I found = the tutorials written by Justin Lemkul quite instructive as a
> star= ting point:
> http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gm= x-tutorials/index.html
>
> Tutorial #2 deals specifically = with building a lipid membrane with a
> peptide solute.
>
> Regards,
> Pablo

Many thanks to both=C2=A0 Richards, to Andreas, Siegfried, and last but no= t least to Pablo for their replies. I have first to say that I am indeed in= terested in carrying out atomistic, classical MD simulations (with GROMACS)= on models of archeal membranes. These membranes differ from eukaryotik one= s in their composition. They consist of bipolar tetraether, macrocyclic, so= called bola lipids, forming monolayers instead of conventional, di-ester l= ipids forming bilayers in the latter. And this is the main issue. I tried = CHARMM GUI, which is really a very useful tool for building membrane models= , but "only" 30 "standard" (diester, or diacylglycerids= ) lipids are=20 available for membrane model building in its library. I asked the developers and got the following feedback from Sunhwan Jo (thanks a lo= t to him too):

> 1. Is it possible to build a homogeneous lipi= d bilayer? The corresponding selection seems to not be active
Yes, j= ust use the lipid composition input box, and put 1 as the ratio
of the lipid type that you would like to build.
> 2. Is it possibl= e to use my own lipids (not conventional di-ester, but di- or tetraether li= pids) by supplying the corresponding PDB fle? Only "conventional"= (phospho)lipids are listed
No, right now, we don't have a method to include custom lipid into the = building
process. However, you can build the bilayer with a lipid type, = and use the input
files generated by the Membrane Builder as a example t= o include your lipid.

I'm currently trying to do the latter, but it's tough. Another = tool, PACKMOL, was also recommended to me. I haven't tried it yet.
Regarding the GROMACS tutorial recommended by Pablo: here a ready DPPC-mem= brane model ("dppc128.pdb - the structure of a 128-lipid DPPC bilayer&= quot; ) is used. My current goal is to build a similar, but monolayer model= , with my own lipid since I don't get it off the shelf. I would have th= en to hydrate it and add alkali and halide ions to it. Lots to do ...

Thank you again for all the helpful contributions and best regards,
=
Felipe
--20cf307f334291e9fb04c39e9d7b--