[gmx-users] POPC in water

Dear gmx users,   I want to simulate a protein in bilayer. The chosen bilayer is POPC. According to Justin's tutorial about KALP15 in DPPC, I would simulate the protein in lipid bilayer and water. In this tutorial I didn't find the simulation of bilayer in water seperately and it is just going

Re: [gmx-users] POPC in water

On 7/10/12 6:09 AM, Shima Arasteh wrote: Dear gmx users, I want to simulate a protein in bilayer. The chosen bilayer is POPC. According to Justin's tutorial about KALP15 in DPPC, I would simulate the protein in lipid bilayer and water. In this tutorial I didn't find the simulation of bilayer

[gmx-users] POPC: ff53a6 and CHARMM36 formats

Hi ALL, I have a equilibrated POPC bilayer (100 ns run) that I have run using GROMOS ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation using CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming conventions (N, P, C, O) between this two FFs as a result of which

Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats

I guess there are better solutions but an alternative is to map your bilayer to MARTINI (http://md.chem.rug.nl/cgmartini/) and then to use SUGAR-PIE (http://smmb.usc.es/sugarpie/sugarpie.php) to go to from MARTINI to all-atom CHARMM36. Hope it helps, Ángel. On Tue, 2012-05-01 at 17:25 +0530,

Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats

On 5/1/12 8:05 AM, Ángel Piñeiro wrote: I guess there are better solutions but an alternative is to map your bilayer to MARTINI (http://md.chem.rug.nl/cgmartini/) and then to use SUGAR-PIE (http://smmb.usc.es/sugarpie/sugarpie.php) to go to from MARTINI to all-atom CHARMM36. Even simpler

Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats

Thanks Angel and Justin. Will try out the options! Regards, -Anirban On Tue, May 1, 2012 at 5:46 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/1/12 8:05 AM, Ángel Piñeiro wrote: I guess there are better solutions but an alternative is to map your bilayer to MARTINI

[gmx-users] POPC bilayer with Charmmff

Dear Gromacs users, I have downloaded the POPC bilayer molecular coordinates with charmmff equilibrated from Dr. Klauda's website. In this site it is mentioned Note: If you run these simulations in NAMD you MUST use NAMD 2.7b3 with vdw ForceSwitching turned on; what does vdw ForceSwitching

[gmx-users] POPC 53a6 topology (dihedral multiplicity)

Hello everyone, I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip ( http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies) for a simple lipid in water sim (gromacs version 4.0.5). I am using the lipid coordinates from the

Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

HAve look at the paper describing the topology ... On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote: Hello everyone, I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip (

Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

Yup, those are indeed constants associated with phi2 (Fig. 1(B)), thanks. Just in case anyone else is faced with the same issue, as far as forces are concerned, these dihedrals can be commented out. When considering the energy associated with dihedrals, just shift it appropriately. On Mon, May 3,

RE: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Alex Smolyanitsky [asmol...@asu.edu] Sent: 03 May 2010 18:22 To: Discussion list for GROMACS users Subject: Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity) Yup, those are indeed constants associated with phi2 (Fig. 1(B)), thanks

Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

:22 To: Discussion list for GROMACS users Subject: Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity) Yup, those are indeed constants associated with phi2 (Fig. 1(B)), thanks. Just in case anyone else is faced with the same issue, as far as forces are concerned, these dihedrals can

Re: [gmx-users] POPC Membrane + protein dynamics

  --- On Sat, 27/3/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] POPC Membrane + protein dynamics To: Gromacs Users' List gmx-users@gromacs.org Date: Saturday, 27 March, 2010, 4:59 PM ravi sharma wrote

Re: [gmx-users] POPC Membrane + protein dynamics

  --- On Sat, 27/3/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] POPC Membrane + protein dynamics To: Gromacs Users' List gmx-users@gromacs.org Date: Saturday, 27 March, 2010, 1:50 AM pa...@ncbs.res.in

Re: [gmx-users] POPC Membrane + protein dynamics

...@vt.edu Subject: Re: [gmx-users] POPC Membrane + protein dynamics To: Gromacs Users' List gmx-users@gromacs.org Date: Saturday, 27 March, 2010, 1:50 AM pa...@ncbs.res.in /mc/compose?to=pa...@ncbs.res.in wrote: hi i have tried as per your justin lemkul's tutorial

Re: [gmx-users] POPC Membrane + protein dynamics

pa...@ncbs.res.in wrote: hi i have tried as per your justin lemkul's tutorial. after aligning the protein with membrane, subsequently we tried to use grompp to generate a tpr file i got the following error. --- Program grompp_mpi, VERSION

Re: [gmx-users] POPC Membrane + protein dynamics

pa...@ncbs.res.in wrote: Dear All, I'm a new comer to gromacs. I need to perform molecular dynamics simulation of my protein within the POPC membrane. I have downloaded the 128a popc lipid from Prof.Tieleman's group along with the required popc.itp. My protein of interest is 458 residues.

Re: [gmx-users] POPC Membrane + protein dynamics

Dear Justin, Many thanks for your comprehensive mail. I will try to do it and let you know if i come across any problem..(Definetely i may bug u again :)) Thank you so much. Best regards Padhu pa...@ncbs.res.in wrote: Dear All, I'm a new comer to gromacs. I need to perform molecular dynamics

[gmx-users] POPC number

Hi gmx-users, whats the number of POPC molecules should be there after inserting protein into popc? In my case 90 popc molecules are there around the protein from 128 molecues which I downloaded from Dr.Tielman's website. Any suggestion will be appreciated Thanks in advance.

Re: [gmx-users] POPC number

I guess that depends on the size of your protein. You should have enough lipds such that the protein doesn't interact with its preriodic image. 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I usually had something like 270 POPE molecules, but if you simulate a smaller

[gmx-users] POPC number

I guess that depends on the size of your protein. You should have enough lipds such that the protein doesn't interact with its preriodic image. 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I usually had something like 270 POPE molecules, but if you simulate a smaller

Re: [gmx-users] POPC number

[EMAIL PROTECTED] wrote: I guess that depends on the size of your protein. You should have enough lipds such that the protein doesn't interact with its preriodic image. 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I usually had something like 270 POPE molecules, but

Re: [gmx-users] POPC number

[EMAIL PROTECTED] wrote: I guess that depends on the size of your protein. You should have enough lipds such that the protein doesn't interact with its preriodic image. 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I usually had something like 270 POPE molecules, but

[gmx-users] POPC structure

Hi all, I found 128 popc lipid molecules in prof Tieleman's website ,I want to work on lipids with more than 128 popc lipid molecules, I knew that with help of VMD generate popc lipid molecules how many number we want. Can anyone suggest anyother website. Thanks in advance.

Re: [gmx-users] POPC structure

You can use genconf to replicate the 128-lipid system any number of times you wish. You can also generate replicates of a subset of these lipids (say if you wanted to replicate only 100 of them) by identifying which residues you want, using genconf, and equilibrating thoroughly. A similar

[gmx-users] popc

Dear gromacs users, I would like to perform simulations of a protein embedded in popc, using a force field of the gromos series and I downloaded popc.pdb, popc.itp, lipid.itpa and the force field ffG43a2x extended for lipids. Looking throughout the archive I found different suggestions, but

Re: [gmx-users] popc

Quoting Chiara Parravicini [EMAIL PROTECTED]: Dear gromacs users, I would like to perform simulations of a protein embedded in popc, using a force field of the gromos series and I downloaded popc.pdb, popc.itp, lipid.itpa and the force field ffG43a2x extended for lipids. Looking

Re: [gmx-users] popc

Thank you for your advice! I reformatted the ffG43a2x.hdb file, but now pdb2gmx is complaining about the ffG43a2x-n.tdb file, that is different from the ffG53a6 one, and probably it would complain also for ffG43a2x-c.tdb. Here, also the fields gd_* don't match. Is there the way to use the

Re: [gmx-users] popc

Quoting Chiara Parravicini [EMAIL PROTECTED]: Thank you for your advice! I reformatted the ffG43a2x.hdb file, but now pdb2gmx is complaining about the ffG43a2x-n.tdb file, that is different from the ffG53a6 one, and probably it would complain also for ffG43a2x-c.tdb. Here, also the fields

[gmx-users] popc

You are experiencing problems because popc is not a protein and pdb2gmx is currently only set up for proteins. More importantly, you already have popc.itp so you don't need to run pdb2gmx on it. I suggest that you read the manual more closely about setting up a simulation and clarify your

Re: [gmx-users] POPC simulation

On Thu, Nov 01, 2007 at 12:36:33PM +, Moutusi Manna wrote: Hi I want to perform peptide + popc membrane simulation. I download popc128a.pdb from (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies). Before I introduce the peptide into the membrane, the water

[gmx-users] POPC simulation

Hi I want to perform peptide + popc membrane simulation. I download popc128a.pdb from (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies). Before I introduce the peptide into the membrane, the water layer had to be broadened to ensure full solvation of the peptide .I

[gmx-users] POPC simulation

Hi I want to perform peptide + popc membrane simulation. I download popc128a.pdb from (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies). Before I introduce the peptide into the membrane, the water layer had to be broadened to ensure full solvation of the

[gmx-users] POPC simulation

Hi I want to perform peptide + popc membrane simulation. I download popc128a.pdb from (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies). Before I introduce the peptide into the membrane, the water layer had to be broadened to ensure full solvation of

[gmx-users] POPC simulation

thanks for reply.I want to perform simulation of popc membrane. Steps which i have done are as follows: 1. download popc128a.pdb, popc.it,lipids.itp (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies) 2. download ffgmx_lipids files 3.convert POPC of .top popc.itp

[gmx-users] POPC simulation

thanks for reply.I want to perform simulation of popc membrane. Steps which i have done are as follows: 1. download popc128a.pdb, popc.it,lipids.itp (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies) 2. download ffgmx_lipids files 3.convert POPC of .top popc.itp

Re: [gmx-users] POPC simulation

Quoting Moutusi Manna [EMAIL PROTECTED]: thanks for reply.I want to perform simulation of popc membrane. Steps which i have done are as follows: 1. download popc128a.pdb, popc.it,lipids.itp (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies) 2. download

Re: [gmx-users] POPC membrane simulations

Hi Chris: I´ve created my own dppc.itp using the ffG53a5 force field. I did that running only a dppc lipid of the membrane that is available on Tieleman's site and i included it on my topology file and of course put in it the number of dppc molecules . i haven´t had any problem with this

[gmx-users] POPC membrane simulations

If I understand correctly you want to construct popc.itp from the dppc.itp that is available on Tieleman's site? And you have used PRODRG to do this? That sounds like a lot of extra work when popc.itp is directly available from Tieleman's site...

[gmx-users] POPC membrane simulations

Hi all: I ´m working on membrane peptides simulation under lipid (POPC, from Peter Tieleman group site) and i want to do a popc.itp file using ffG53a5 force field. Some days ago i was working with dppc membranes and i took one lipid and run it through pdb2gmx, using my favourite force field

[gmx-users] POPC membrane simulation (popc.itp)

Hi all: I ´m working on membrane peptides simulation under lipid (POPC, from Peter Tieleman group site) and i want to do a popc.itp file using ffG53a5 force field. Some days ago i was working with dppc membranes and i took one lipid and run it through pdb2gmx, using my favourite force field

Re: [gmx-users] POPC simulation

Hi all,I had similar problem with Fatal errors with Atomtype LC3 not found while setting up a POPC simulation. After a day of trying out different things I figured out the problem. And I would like to share my experience in the mailing list. Renaming of POP to POPC in the .gro files doesn't

[gmx-users] POPC simulation

I previously posted my modifications to get POPE to work with OPLSAA. You could make the analogous changes to your system. The message was: [gmx-users] lipid.itp LJ-1,4 values involving water Wed May 3 20:44:51 CEST 2006 ___ gmx-users mailing list

[gmx-users] POPC simulation

Hi All,thanks to Steffan , Jim and Kaushal for helping me out in the POPC simulation setup. i finally got everything to work. i guess the imp thing was to change the POPC to POP in .top file. thanks once again.Arindam Ganguly ___ gmx-users mailing list

[gmx-users] POPC simulation

Hi Steffen, thanks for the reply. this is what i have done. my topol.top looks like this now #inlcude ffgmx.itp inlcude popc.itp. as per your last reply i have copied the contents of lipid.itp to ffgmxbon.itp and ffgmxnb.itp without removing the contents of the respective file. basically just

Re: [gmx-users] POPC simulation

Arindam, I fixed this problem a while ago and it was pretty difficult to figure out. I tinkered with so many things, once I got it to work I didn't even know what steps I took to fix it! Here's something to try: GROMACS doesn't like the fact popc.itp has a four-character residue name

Re: [gmx-users] POPC simulation

? Is this a bug or I'm missing something? P.S. I run all these tests with gromacs 3.3.1 -- Message: 6 Date: Wed, 24 May 2006 12:02:43 -0500 From: Arindam Ganguly [EMAIL PROTECTED] Subject: [gmx-users] POPC simulation To: gmx-users@gromacs.org Message-ID: [EMAIL

Re: [gmx-users] POPC simulation

Hi Arindam, you've simply got to switch two lines in the *.top file: lipid.itp has to be called by the topology before popc.itp, as it contains the information on atomtypes for GROMACS. So: #include lipid.itp #include popc.itp should work just fine. Greetings Steffen -- Dipl.-Chem. Steffen

[gmx-users] POPC simulation

Hi Steffen,Thanks very much for the prompt reply. i made the changes as mentioned such that my popc.top looks like this :-#include ffgmx.itp#include lipid.itp#include popc.itp #include ffgmx2nb.itp#include ffgmx2bon.itphowever is still get the same message Fatal error: Bonded/nonbonded atom type

[gmx-users] POPC simulation

Hi gmx-users,i am trying to run a POPC simulation. this is what i have done. i downloaded the popc128apdb, lipid.itp , popc.itp files from the following website http://moose.bio.ucalgary.ca/index.php?page=Downloads then i also downloaded the ffgmx_lipids files from the gromacs website.i have

Re: [gmx-users] popc

Shalom, Try make_hole.pl -f input.pdb -o output.pdb -r 1.2 -lipat P -lipid POP Itamar P.S. look at the pdb file for the atom name of the phosphate atom. I use DMPC so it is P, but it is also might be P8 or such. MGiò wrote: Ooops! I mean, I'm using popc.itp, of course! bye, MG On

Re: [gmx-users] popc

Hi!I'm using the popc.top which I have downloaded from this websitehttp://moose.bio.ucalgary.ca/index.php?page=Downloadsand the forcefield I'm using is ffgmx, gromacs forcefield. Cheers,MGOn 5/2/06, mahbubeh zarrabi [EMAIL PROTECTED] wrote: hiI try to use make_hole program to make a hole in