[gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

Tue Jun 7 19:18:08 CEST 2016

Hi Nidhin,

As I understand, it would simply mean copying the line of DOPC, change the
name to DOPAT, replace NC3 by a dash (-) and replace PO4 with NC3.

Cheers,

Tsjerk
On Jun 7, 2016 6:21 PM, "Nidhin Thomas" <nidhin.thomas0624 at gmail.com> wrote:

> Hi Dr. Wassenaar,
>
> Thanks a lot for offering help to create DPPC-DOTAP bilayer model.
>
> I have gone through the research paper on insane method.
>
> I understand that I may be able to create DOTAP template by taking the
> fatty acids and linkers from DOPC lipid template and link them with NC3
> head group.
>
> But I don’t know whether this is correct or how to execute this in
> insane.py.
>
> Could you please guid me through the process of creating the template?
>
> Thanks,
>
> Nidhin Thomas
> University of Houston
>
>
> > On Jun 7, 2016, at 12:51 AM,
> gromacs.org_gmx-users-request at maillist.sys.kth.se wrote:
> >
> > Send gromacs.org_gmx-users mailing list submissions to
> >       gromacs.org_gmx-users at maillist.sys.kth.se
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >       https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or, via email, send a message with subject or body 'help' to
> >       gromacs.org_gmx-users-request at maillist.sys.kth.se
> >
> > You can reach the person managing the list at
> >       gromacs.org_gmx-users-owner at maillist.sys.kth.se
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gromacs.org_gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> >   1. Re: Position restrain of of different chain in fibril
> >      structure (Md. Imrul Reza Shishir)
> >   2. cannot output all the structures of one cluster (Zhenyu Meng)
> >   3. Re: Non-bonded energy (ABANTIKA PAL)
> >   4. Re: gmx gangle selections help (Teemu Murtola)
> >   5. Re: DPPC-DOTAP Mixed Lipid Bilayer (Tsjerk Wassenaar)
> >   6. How to fix the ends of the protein? (Seera Suryanarayana)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Tue, 7 Jun 2016 12:32:14 +0900
> > From: "Md. Imrul Reza Shishir" <imrul.reza.shishir at gmail.com>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Position restrain of of different chain in
> >       fibril  structure
> > Message-ID:
> >       <CANhR7-pzJR2U3CWQb=
> F1S5vhRSNC-xCvtsM8rU4EimXKJtmvsQ at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Dear all
> > good day.
> >
> > https://drive.google.com/open?id=0B9FUC_dv9IRoTUdHZENEN1FaOHc
> >
> > In the google drive file i attached all the file with forcefield file. I
> > only deleted the nvt.trr file. As this file size very big.
> >
> > In this run i only use 7 chain of cellulose. to small the calculation
> step.
> >
> > Still after the energy minimization. When i run the nvt.mdp then the
> fibril
> > structure broken. All chain aligned one by one.
> >
> > Best regards
> >
> > Md Imrul Reza Shishir
> >
> >
> > On Tue, Jun 7, 2016 at 10:19 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 6/6/16 9:13 PM, Md. Imrul Reza Shishir wrote:
> >>
> >>> Dear all
> >>> I have a structure file of cellulose nano fibril of 36 chain (each
> have 40
> >>> residue). I want to simulate it as a single compound. I try to run the
> >>> simulation with OPLS-AA force field. After energy minimization when i
> run
> >>> the equilibrium step then the fibril structure broken and all the chain
> >>> aligned in a single chain like structure. I want to restrain the
> position
> >>> of chain in there original sheet like structure. But I am  not able to
> >>> define.
> >>>
> >>> In the dropbox i attached my simulation structure image file.
> Initially,
> >>> it
> >>> was 7 sheet of 36 cellulose chain (each chain 40 residues). I check the
> >>> structure (gro file) every stage in VMD after new box creation,
> solvating,
> >>> energy minimization. The initial structure is not broken. But after
> >>> equilibrium stage when I run nvt.mpd it will break it initial stage.
> And
> >>> all 36 chain aligned like output structure.
> >>>
> >>> *gmx_mpi pdb2gmx -f (filename).pdb -o (filename).gro -water spce
> -missing*
> >>>
> >>> *gmx_mpi editconf -f test_fibril_processed.gro -o
> >>> test_fibril_newbox.gro -c -d 1.0 -bt cubic *(This box set-up command)
> >>>
> >>> I also attached nvt.mdp, npt.mdp and md.mdp file. This simulation is
> >>> trial run for long time simulation. How should i restrain the position
> >>> of my structure.
> >>>
> >>>
> >>> In the dropbox link i attached nvt.mdp, npt.mdp, md.mdp and also Input
> >>> and output structure image in vmd.
> >>>
> >>>
> https://www.dropbox.com/sh/skkskzp1pruf227/AADI2a7TG6pzadFzIEE8094na?dl=0
> >>>
> >>> Thank you very much.
> >>>
> >>>
> >> Please upload the actual coordinate files and any relevant topologies.
> I
> >> don't see how setting up that structure in a cubic box would lead to
> such a
> >> structure.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >
> >
> >
> > --
> > *Md Imrul Reza Shishir*
> > Master Student
> > *Inha University*
> > *CRC for NanoCellulose Future Composites*
> > 36 Getbeol-ro, Yeonsu-gu
> > Incheon 21999
> > South Korea
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Tue, 7 Jun 2016 12:20:39 +0800
> > From: Zhenyu Meng <fdmm1989 at gmail.com>
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] cannot output all the structures of one cluster
> > Message-ID:
> >       <CAJffFwZrvPn=ogt0uREv=
> L5VYamZkP2Khuxh_sBN8wpsXt9VFQ at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Dear GMX users,
> > I want to output all the structures of certain cluster using g_cluster,
> and
> > the following is my command:
> > g_cluster -f md5_mol.xtc -s md5.tpr -n index.ndx -o md5.xpm -g
> > md5_cluster.log -cutoff 0.12 -cl cluster1.gro -wcl 1 -nst 30
> > While it seems gromacs cannot generate all the structures. Instead, in
> > cluster1.gro there're only several central structures.
> > The .log file is like this:
> > Writing middle structure for each cluster to cluster1.gro
> > Writing all structures for the first 1 clusters with more than 30
> > structures to cluster1.gro%01d.gro
> > But I cannot find cluster1.gro%01d.gro in my directory.
> > Is there anyone knowing what's going on?
> > Your help will be highly appreciated!
> >
> > --
> > Sincerely,
> > Mr. Meng Zhenyu
> > Division of Chemistry and Biological Chemistry
> > School of Physical and Mathematical Sciences
> > Nanyang Technological University
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Tue, 7 Jun 2016 09:53:24 +0530 (IST)
> > From: ABANTIKA PAL <abantikapal at iitkgp.ac.in>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Non-bonded energy
> > Message-ID:
> >       <197569204.6017764.1465273404183.JavaMail.zimbra at iitkgp.ac.in>
> > Content-Type: text/plain; charset=utf-8
> >
> > Hi,
> >
> > So, for calculating non-bonded energy, we have to consider all pair of
> atoms of the protein which are separated by a distance less than the cutoff
> distance. Please correct me if I am wrong.
> >
> > ----- Original Message -----
> > From: "Justin Lemkul" <jalemkul at vt.edu>
> > To: gmx-users at gromacs.org
> > Sent: Tuesday, June 7, 2016 6:50:32 AM
> > Subject: Re: [gmx-users] Non-bonded energy
> >
> >
> >
> > On 6/6/16 9:00 AM, ABANTIKA PAL wrote:
> >> Hi,
> >>
> >> I want to know which atoms are to be considered while calculating
> non-bonded energy of a protein. Whether it is all pair atom or there is a
> particular criteria while selecting the atoms.
> >>
> >
> > The nonbonded energy of a protein would imply that any interactions
> within the
> > defined cutoffs would be included.  Of course, such a quantity is not
> physically
> > meaningful, but that's how it's calculated.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Tue, 07 Jun 2016 04:50:43 +0000
> > From: Teemu Murtola <teemu.murtola at gmail.com>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] gmx gangle selections help
> > Message-ID:
> >       <CAB5URpbOkXv_=
> u__jyFjRMc7b39KnS-P9Y0_YuFgnhdqqN+tiQ at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi,
> >
> > Your selection should produce what you want, assuming that each LIG
> residue
> > has exactly one A and one B atom. The center-of-mass is calculated from A
> > and B atoms only, and then both of them are selected or not as a single
> > unit. Is there something in the documentation that could be clarified to
> > make this clearer?
> >
> > Teemu
> >
> > On Mon, Jun 6, 2016, 16:54 Eric Smoll <ericsmoll at gmail.com> wrote:
> >
> >> Hello gromacs users,
> >>
> >> I want to map the angle between a specific bond vector (defined by the
> >> atoms A and B) and the z axis using gmx gangle. I am only interested in
> >> bond vectors that have a center-of-mass z-coordinate greater than C. Is
> >> there a way to make this selection using the 'gmx select'-type
> statements?
> >> I suspect that the selection below will not produce an appropriately
> paired
> >> set of bond atoms. Am I correct?
> >>
> >> -g1 vector
> >> -g2  z
> >> -group1 ''resname LIG and name A B and part_res_com z > C"
> >>
> >> Best,
> >> Eric
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Tue, 7 Jun 2016 07:26:27 +0200
> > From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Subject: Re: [gmx-users] DPPC-DOTAP Mixed Lipid Bilayer
> > Message-ID:
> >       <
> CABzE1SiGL9CrVOZe+tzMxV77V8bGJOdxx6rT8hAFMPv5LJpXvg at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi Nidhin,
> >
> > Insane allows you to build lipids from the command line. Alternatively,
> > it's pretty easy to add DOTAP to insane, using the templates inside. If
> you
> > feel you need a hand with that, let me know.
> >
> > Cheers,
> >
> > Tsjerk
> > On Jun 7, 2016 12:21 AM, "Nidhin Thomas" <nidhin.thomas0624 at gmail.com>
> > wrote:
> >
> >> Hi GROMACS Users,
> >>
> >> I would like to create a mixed bilayer of DPPC and DOTAP lipids for
> >> research. I usually use charm-gui or insane.py to create a mixed
> bilayer.
> >> But I could not find DOTAP listed in either of these lists. When I
> searched
> >> online, I got a mixed bilayer system for DMPC & DPPC lipids and the
> >> parameter file for DOTAP lipid from
> >> http://www.softsimu.net/downloads.shtml.
> >>
> >> My objective is to create mixed lipid bilayer system with various
> >> percentage of DOTAP lipids. In addition, I have to create a bilayer with
> >> one DOTAP in each layer and remaining DPPC lipids. Can anyone please
> guide
> >> me to create these lipid bilayers? It would be great if someone could
> >> explain, how to create these mixed bilayers from scratch.
> >>
> >> Thanks a lot everyone!,
> >>
> >> Nidhin Thomas
> >> University of Houston
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Tue, 7 Jun 2016 11:21:45 +0530
> > From: Seera Suryanarayana <palusoori at gmail.com>
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] How to fix the ends of the protein?
> > Message-ID:
> >       <CAAr94NP=k_LKUvOpmg=
> U0wAnAvo3K5x472FGyKwFTiBq_Aguaw at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Dear Gromacs users,
> >
> > I would like to simulate the topological domain of one protein. For that
> I
> > need to fix the ends of the simulated protein. How do one can
> > fix(constraint) the ends of the protein? Kindly help me how to do this
> > fixation?
> >
> > Surya
> > Graduate student
> > India.
> >
> >
> > ------------------------------
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> >
> > End of gromacs.org_gmx-users Digest, Vol 146, Issue 27
> > ******************************************************
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.