Re: [gmx-users] Embedding Protein into lipid bilayer

On 2/22/16 4:40 AM, khourshaeisha...@mech.sharif.ir wrote: Dear Justin Thanks for your reply. I think, I got what you mean. By the way, My protein needs to use BGL residue and of course this type of the residue isnt available in the gromacs sources. So I find its informati

[gmx-users] Embedding Protein into lipid bilayer

Dear Justin Thanks for your reply. I think, I got what you mean. By the way, My protein needs to use BGL residue and of course this type of the residue isnt available in the gromacs sources. So I find its information in ATP site and it is attached to my Email as a .itp file. I

Re: [gmx-users] Embedding Protein into lipid bilayer

On 2/21/16 5:44 AM, khourshaeisha...@mech.sharif.ir wrote: p { margin-bottom: 0.1in; line-height: 120%; }a:link { } Dear Justin first of all, thanks for your replay. but I should cite that the bizarre character that you saw in my Email was Sharif university Email domains

[gmx-users] Embedding Protein into lipid bilayer

p { margin-bottom: 0.1in; line-height: 120%; }a:link { } Dear Justin first of all, thanks for your replay. but I should cite that the bizarre character that you saw in my Email was Sharif university Email domains fault not me. also different copies of Email was because of th

Re: [gmx-users] Embedding Protein into lipid bilayer

Please don't spam the list with many copies of the same message. People give of their free time to answer questions on the list, so it may take a while for someone to respond. Please also make sure your emails are legible; yours are littered with bizarre characters. On 2/20/16 5:30 AM, kho

[gmx-users] Embedding Protein into lipid bilayer

Hi Catarina Thanks for your reply, I really appreciate it. you know, I complete Justin's Tutorial, so I know what procedures I should do. but now I want to embed 2rh1 protein into DPPC lipid bilayer� which I already downloaded it from rcsb.com.� when I tried to use pdb2gmx� vi

[gmx-users] Embedding Protein into lipid bilayer

pre.cjk { font-family: "Nimbus Mono L",monospace; }p { margin-bottom: 0.1in; line-height: 120%; }a:link { } Hi Catarina Thanks for your reply, I really appreciate it. you know, I complete Justin's Tutorial, so I know what procedures I should do. but now I want to embed 2rh1

[gmx-users] Embedding Protein into lipid bilayer

Dear All During researching Internet, I found justin and Anirban's tutorial about embedding protein in lipid membrane. It was useful and I appreciate them but I had one question.

Re: [gmx-users] Embedding Protein into lipid bilayer

You can also use g_membed (a GROMACS tool) for the protein insertion. In the latest GROMACS versions g_membed is part of the mdrun tool (-membed flag). The reference is Wolf_2010_JC g_membed is easily combined with LAMBADA as well. On 19

Re: [gmx-users] Embedding Protein into lipid bilayer

Hi Ali, First create the topology for the protein alone using pdb2gmx. Then, and if you already have a pre-equilibrated membrane patch, perform the protein alignment and insertion into the membrane. There are several ways to do this (see below). Align the protein with the membrane: - manual proc

[gmx-users] Embedding Protein into lipid bilayer

Dear All During researching Internet, I found justin and Anirban's tutorial about embedding protein in lipid membrane. It was useful and I appreciate them but I had one question. as I understood, I should make some changes to protein pdb file ( 1r2h for Ex) before using it in pdb2gmx command o

Re: [gmx-users] Embedding protein into lipid bilayer

Justin Lemkul writes: > > > On 3/6/15 11:02 PM, yoochan wrote: > > Dear GMX users, > > > > I’m tyring to build lipid and transmembrane(protein) system using > > inflategro.pl. in GROMACS 5.0.4. > > > > I think the inflategro.pl can not build a result on center of box when the > > membrane or

Re: [gmx-users] Embedding protein into lipid bilayer

On 3/6/15 11:02 PM, yoochan wrote: Dear GMX users, I’m tyring to build lipid and transmembrane(protein) system using inflategro.pl. in GROMACS 5.0.4. I think the inflategro.pl can not build a result on center of box when the membrane or lipid are quite large. That's not likely true. He

[gmx-users] Embedding protein into lipid bilayer

Dear GMX users, I’m tyring to build lipid and transmembrane(protein) system using inflategro.pl. in GROMACS 5.0.4. I think the inflategro.pl can not build a result on center of box when the membrane or lipid are quite large. Here is my workflow 1. Prepare a protein (1R3J) 2. Prepare a optimi