Re: [gmx-users] problem in simulation of lipid bilayer

It is probably best to fix your lipid bilayer problem first. Inserting a protein won't fix the problem(s). XAvier On Mar 31, 2009, at 8:05, nitu sharma wrote: Dear all, I am trying to simulation of membrane proteins I have a basic question can we directly go for sim

[gmx-users] Fwd: No plot found running .xvg files using xmgrace produced by g_helix.

-- Forwarded message -- From: Chitrita Dutta Roy Date: Mon, Mar 30, 2009 at 9:42 PM Subject: No plot found running .xvg files using xmgrace produced by g_helix. To: gmx-users Dear gromacs user, I am stuck in a problem with g_helix command. The output of the g_helix is and a s

Re: [gmx-users] problem in simulation of lipid bilayer

Dear Nitu madam, You can directly go for simulation of lipid+protein complex if u r using a pre-equilibrated bilayer as from Dr. Tieleman's website. Regards, Pawan 2009/3/31 nitu sharma > Dear all, > > I am trying to simulation of membrane proteins I have a > basic question

[gmx-users] problem in simulation of lipid bilayer

Dear all, I am trying to simulation of membrane proteins I have a basic question can we directly go for simulation of lipid+protein complex without doing simulation of individually simulation of lipid bilayer because I am facing lot of problem with topology file for lipid bila

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir, Greetings from Pawan. I have used force constants of 10 in position restraint .itp files for proteins as suggested in Dr. Tieleman' s webisite for Inflategro. The mdp files are : *For energy minimization:* title = Protein in DPPC Bilayer cpp = /u

RE: [gmx-users] grompp error in running simulation of lipid bilayer

Might I suggest that you refer to this webpage http://wiki.gromacs.org/index.php/Errors It would have answered both of your error questions you have posted. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University

[gmx-users] Elastic Network Model

I am interested in potentially using gromacs to do some calculations on an C-alpha based elastic network model of the protein that I'm working on. I'm curious if other users have done similar types of calculations, and if so, what protocol you used. I realize that there are a lot of webserv

Re: [gmx-users] solvent box outside protein

No, not this one again! Why not search the archives? Or browse the wiki? Or follow a more extensive tutorial on Gromacs: http://nmr.chem.uu.nl/~tsjerk/course/molmod/ ? Tsjerk 2009/3/30 Halie Shah : > > Hi, > > I just finished my energy minimization run on GROMACS 4.0.4 for my > ligand/protein co

Re: [gmx-users] POPE setup

On Mon, Mar 30, 2009 at 06:43:37AM -0600, Peter Tieleman wrote: > Hi, > > I noticed several comments on problems with POPE in vacuum. I haven't > made POPE systems in quite a while, but perhaps it would be an idea to > temporarily set the charge of the H-atoms on the NH3+ group to zero, or > ad

[gmx-users] solvent box outside protein

Hi, I just finished my energy minimization run on GROMACS 4.0.4 for my ligand/protein combination. I opened the minimized protein pdb and the original pdb in VMD to visualize, but saw that my minimized protein was outside the solvent box I had made. How should this be corrected? Below is what I sp

[gmx-users] how to define the dummy atoms in gromacs

Hi all users, I need to add some dummy atoms in my case. I know that I need to include the section [virtual_sites] in the top file but I am not sure how to define them in the itp file .Do I need to list these atoms in the section[atoms] ? Can anyone of you give me some suggestions about that?

Re: [gmx-users] Missing atom in residue

Jack Shultz wrote: Hi, What are some of the ways used to fix these problems? Do you manually manipulate these files to add missing residues or are there any automated methods? I tried ignoring it with -missing, which is probably a bad way to treat this error. Still that did not ignore the erro

[gmx-users] Missing atom in residue

Hi, What are some of the ways used to fix these problems? Do you manually manipulate these files to add missing residues or are there any automated methods? I tried ignoring it with -missing, which is probably a bad way to treat this error. Still that did not ignore the error. Does this require a

Re: [gmx-users] new block lactitol

ceste...@unsl.edu.ar wrote: Hi All I am trying to analize the dynamics of polysaccharid which include lactitol grups (b-D-Galp-(1-4)-D-Glc-ol), using ffG53a6 force field. I need to make a new building block in .rtp file, but I don´t know about the proper parameters. Most of the fundamental bu

Re: [gmx-users] Prepping Docking Complexes

Jack Shultz wrote: Hi Guys, Thanks for previous help. Especially Justin. I got the amber03 and tip3 water models working through my BOINC project now. But if I want to simulate a docking complex, I'm running to some errors preparing it. I have not done extensive research on this yet, but I'm w

[gmx-users] Prepping Docking Complexes

Hi Guys, Thanks for previous help. Especially Justin. I got the amber03 and tip3 water models working through my BOINC project now. But if I want to simulate a docking complex, I'm running to some errors preparing it. I have not done extensive research on this yet, but I'm wondering how I can prep

[gmx-users] No plot found running .xvg files using xmgrace produced by g_helix.

Dear gromacs user, I am stuck in a problem with g_helix command. The output of the g_helix is and a sample of the resultant .xvg files are attached here. There is no plot found when I ran resultant .xvg files by xmgrace. What are the problems here? Please help me out. Thanks in advance. Chit

[gmx-users] new block lactitol

Hi All I am trying to analize the dynamics of polysaccharid which include lactitol grups (b-D-Galp-(1-4)-D-Glc-ol), using ffG53a6 force field. I need to make a new building block in .rtp file, but I don´t know about the proper parameters. Someone has made a lactitol´s block or can help me with the

Re: [gmx-users] Error with equilibration of DPPC membrane with protein

Hi again an Thank you for comments! Justin A. Lemkul wrote: Edvin Erdtman wrote: Hi We have a problem of equilibrate the system with a protein within DPPC. We have used dppc128.pdb from Dr. Tielemans website. We have been using their perl script inflategro.pl to insert our protein. We used

[gmx-users] POPE setup

Hi, I noticed several comments on problems with POPE in vacuum. I haven't made POPE systems in quite a while, but perhaps it would be an idea to temporarily set the charge of the H-atoms on the NH3+ group to zero, or add exclusions between the H atoms and the phosphate oxygens. I haven't trie

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. I did the Inflategro procedure for the POPC bilayer generated using genconf. It took around 26 compressions for coming near the initial area (just above it). The minimization were all converged to Fmax < 1350. If I decrease the Fmax les

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir, Greetings from Pawan. I did the Inflategro procedure for the POPC bilayer generated using genconf. It took around 26 compressions for coming near the initial area (just above it). The minimization were all converged to Fmax < 1350. If I decrease the Fmax less than this I am getting

Re: [gmx-users] water model and force field

varsha gautham wrote: Dear gmx-users, Am doing a simulation of DPPC bilayer with a polymer. I read from various papers that SPC is the best water model for lipids and GROMOS 87 is the best force field adapted for the lipids. So i made use of SPC and gromos 87 in my simulation .But am not cle

Re: [gmx-users] Error with equilibration of DPPC membrane with protein

Edvin Erdtman wrote: Hi We have a problem of equilibrate the system with a protein within DPPC. We have used dppc128.pdb from Dr. Tielemans website. We have been using their perl script inflategro.pl to insert our protein. We used position restraints for the protein as mentioned in Methods

Re: [gmx-users] grompp errors

No. Even though you give the grompp output, you haven't told what you tried to do, which force field you're using and what you did to come to this stage. We can't guess what's in you're topology file. You also clearly haven't searched the archive for posts on "No default ... types", and thus give

[gmx-users] water model and force field

Dear gmx-users, Am doing a simulation of DPPC bilayer with a polymer. I read from various papers that SPC is the best water model for lipids and GROMOS 87 is the best force field adapted for the lipids. So i made use of SPC and gromos 87 in my simulation .But am not clear with GROMOS 87 file for

[gmx-users] grompp errors

i have a problem with gromp someone can elp me? thanks.. error_grompp Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/

Re: [gmx-users] grompp error in running simulation of lipid bilayer

Hello Madam, Greetings from Pawan. The solution for this is to edit the atom names as required such as replace NTM with N4 in all the places wherever NTM occurs. Similarly do this for all the atoms of the dppc lipid. I think this is a probable solution. I dont know how far I am right. Regards, P

[gmx-users] grompp error in running simulation of lipid bilayer

Hi pawan , Thanks for your right suggestion bu t after editing lipid.itp the another error comes like this- processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp Opening library fi

[gmx-users] Error with equilibration of DPPC membrane with protein

Hi We have a problem of equilibrate the system with a protein within DPPC. We have used dppc128.pdb from Dr. Tielemans website. We have been using their perl script inflategro.pl to insert our protein. We used position restraints for the protein as mentioned in Methods 41 (2007) 475-488. We ha

[gmx-users] Re: Water models for amber03 (Justin A. Lemkul)

ile lipid.itp, line 9 > Last line read: > '1 1' > Found a second defaults directive. > > my command line like this- [n...@localhost dmpc1tap]$ grompp -f em.mdp -p > dmpc.top -c dmpc-solvated.pdb -o dmpc-em.tpr > If anyone