[gmx-users] DPPC-DOTAP Mixed Lipid Bilayer
Nidhin Thomas
nidhin.thomas0624 at gmail.com
Tue Jun 7 18:20:51 CEST 2016
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:
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> 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
>>
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>
>
>
> --
> *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!
>
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>
> ------------------------------
>
> 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
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>> posting!
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>
>
> ------------------------------
>
> 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!
>>
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>> 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.
>
>
> ------------------------------
>
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