[gmx-users] Charge assignment

Hi everyone.   I'm working on getting parameters for a protein system that has some linker residues in it.  These linkers are nothing too strange, they just have some amine groups.  I can get bonded parameters from the prodrg server.  I know the charge groups are unreliable.  I'm using the 53A6

[gmx-users] asking help for simulation of protein in 8M urea

Dear all, I want to a protein simulation in 8M urea. Can anyone suggest me any introductory tutorial on that. Thank you in advance. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] Re: [gmx-user]Error by pdb2gmx (Mark Abraham)

Hi, Please leave some context in your email replies. Whoever replied last time has their own work and probably responded to other people's problems on here... They won't remember your context as well as you do :-). IIRC, I pointed out the problem was probably in what you'd done with the .rtp

Re: [gmx-users] asking help for simulation of protein in 8M urea

On 05/20/2010 09:05 AM, caty hacker wrote: Dear all, I want to a protein simulation in 8M urea. Can anyone suggest me any introductory tutorial on that. Thank you in advance. I think a tutorial is useless for such a simulation. Papers are the best reference depending on what you

[gmx-users] adding constraints

Hi all, I want to add constraints for bond length of a ligand.Where do I place the constraints statement in the .rtp file or in the .top file?   Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] g_helixorient issue

Hi ALL, I am trying to find out the tilt of a helix during a simulation. I am using g_helixorient with the -otilt option. However I am getting the following output, which when plotted using xmgrace, gives a straight along y=0.

Re: [gmx-users] asking help for simulation of protein in 8M urea

Hi Caty, In addition to Luca's comments, also consider what you mean with 8M. Molarity is defined as mole per liter, but the addition of urea may have an effect on the volume, such that adding a volume x urea to a volume y water does not yield a volume x+y. Especially with such high

Re: [gmx-users] DSSP

Hi Shahid, I have fixed the problem in do_dssp. You can either pull the newest release-4-0-patches branch from the git repository or change ./src/tools/do_dssp.c, line 80 from snew(ssbuf,nres+10); to: snew(ssbuf, 2*nres-1); Carsten On May 19, 2010, at 9:48 AM, Carsten Kutzner wrote:

[gmx-users] g_helixorient issue

Hi ALL, I am trying to find out the tilt of a helix during a simulation. I am using g_helixorient with the -otilt option. However I am getting the following output, which when plotted using xmgrace, gives a straight along y=0.

[gmx-users] Essential Dynamics

Hi everyone, Please I need a piece of information not related to gromacs. I'm searching for a document or article that may explain Essential Dynamics to beginners. Thanks Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] Essential Dynamics

On 05/20/2010 10:40 AM, Carla Jamous wrote: Hi everyone, Please I need a piece of information not related to gromacs. I'm searching for a document or article that may explain Essential Dynamics to beginners. Thanks Carla http://www.ncbi.nlm.nih.gov/pubmed/8108382 AKA how the molecular

Re: [gmx-users] Essential Dynamics

On 05/20/2010 10:40 AM, Carla Jamous wrote: Hi everyone, Please I need a piece of information not related to gromacs. I'm searching for a document or article that may explain Essential Dynamics to beginners. Thanks Carla and of course, in a more practical way:

Re: [gmx-users] Re: acetonitrile from amber to gromacs

Alan schrieb: Dear Vedat, On Wed, May 19, 2010 at 20:36, gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org wrote: @rui acpypi -i ch3cn_210.pdb says: cannot find template for residue C3N in our library. and indeed, there's no residue C3N in my

[gmx-users] Re: Re: energy decreasing in NVE simulation

Dear Erik, Thank you so much for your prompt reply. I appreciate it. Yun-an Yan Erik Marklund writes: For more exotic NVE-systems I had to do some or several of the following things to get stable Etot: * have an even shorter timestep than one would expect from the applied constraints and

Re: [gmx-users] Re: Re: energy decreasing in NVE simulation

Hi Yun-an Yan, In addition to the other things, COMM removal is also a source of energy drift. It is better to center your solute afterwards. Cheers, Tsjerk On Thu, May 20, 2010 at 1:05 PM, Yan Yun-an yun-an@uni-rostock.de wrote: Dear Erik, Thank you so much for your prompt reply. I

[gmx-users] g_helixorient issue

Hi ALL, I am trying to find out the tilt of a helix during a simulation. I am using g_helixorient with the -otilt option. However I am getting the following output, which when plotted using xmgrace, gives a straight along y=0.

Re: [gmx-users] breaking down total energy

Moeed wrote: Hello Justin, Thanks for your comments. Actually, since I am interested in only interaction energies *between* molecules I thought by excluding energies between atoms on a single chain what I get from nonbonded interactions would not include 1-4 interactions. OK, I see

Re: [gmx-users] Charge assignment

Michael McGovern wrote: Hi everyone. I'm working on getting parameters for a protein system that has some linker residues in it. These linkers are nothing too strange, they just have some amine groups. I can get bonded parameters from the prodrg server. I know the charge groups are

Re: [gmx-users] adding constraints

subarna thakur wrote: Hi all, I want to add constraints for bond length of a ligand.Where do I place the constraints statement in the .rtp file or in the .top file? Are you looking to constrain only one single bond length? If so, just add a [constraints] section to your topology. The

Re: [gmx-users] enegry minimisation

Hello Gaurav, Thanks for your reply, I did position restrained enegry minimisation, and used following .mdp file for the same title    =  protein cpp  =  /usr/bin/cpp ; the c pre-processor define   =  -DPOSRE constraints  =  none integrator   =  steep dt   

[gmx-users] g_bundle issue

Hi ALL, I tried to calculate the helix tilt of a single helix (TM5) among 7 helices using g_bundle. In the index file I defined the two groups (top bottom) as the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in the bun_tilt.xvg file I am getting the values as:

Re: [gmx-users] Re: OPLS-AA/L force field

The force fields have to be compatible but this way works fine. On 19 May 2010 12:50, Justin A. Lemkul jalem...@vt.edu wrote: Oliver Grant wrote: Can you not run pdb2gmx for each of your molecules that you want separate force fields for? Then cat the gro files, renumber and include the

Re: [gmx-users] enegry minimisation

sonali dhindwal wrote: Hello Gaurav, Thanks for your reply, I did position restrained enegry minimisation, and used following .mdp file for the same title= protein cpp = /usr/bin/cpp ; the c pre-processor define = -DPOSRE constraints = none

Re: [gmx-users] Re: OPLS-AA/L force field

Oliver Grant wrote: The force fields have to be compatible but this way works fine. I guess that depends on what you mean by works fine. If you mean that you can produce a stable simulation, then yes, it may work, but I would question the underlying premise of combining different force

Re: [gmx-users] enegry minimisation

Can you try using g_rms to compare the difference between the structures before and after EM. -Gaurav On Thu, May 20, 2010 at 7:53 AM, Justin A. Lemkul jalem...@vt.edu wrote: sonali dhindwal wrote: Hello Gaurav, Thanks for your reply, I did position restrained enegry minimisation, and

Re: [gmx-users] Re: OPLS-AA/L force field

*I guess that depends on what you mean by works fine. * I mean the method of using pdb2gmx to generate a top and gro and then appending the gro files and including the .itp files in the .top file, works if you want to use two force fields. Originally I thought that was the question. *I guess it

[gmx-users] Re: acetonitrile from amber to gromacs

Nice, glad you did progress. See below. On Thu, May 20, 2010 at 12:38, gmx-users-requ...@gromacs.org wrote: thanks for your helpful hints. i updated acpype, created a pdb file with a single molecule and ran acpype -i ch3cn_210_single.pdb which generated an .itp and other interesting files.

[gmx-users] Re: OPLS-AA/L force field

Dear Oliver, On Thu, May 20, 2010 at 13:21, gmx-users-requ...@gromacs.org wrote: I'm using GLYCAM06, so it involves a bit more effort to generate a .top and .gro file than just using pdb2gmx but I thought I'd leave it out as I just wanted to explain the method I use to include it. Apologies

Re: [gmx-users] Re: OPLS-AA/L force field

*If you are familiar to ambertools (tleap mainly), so you can create your molecule there, save the amber parameters and use acpype to convert from amber to gromacs format. *Thanks Alan, I use tleap and then amb2gmx.pl. It works great, the only problem is the NAc groups aren't restrained properly

Re: [gmx-users] enegry minimisation

Hello Gaurav, when i did g_rms with structre before energy minimisation as refrence and strucutre after energy minimisation, it came to be around 0.02. -- Sonali Dhindwal --- On Thu, 20/5/10, Gaurav Goel gauravgoel...@gmail.com wrote: From: Gaurav Goel gauravgoel...@gmail.com Subject: Re:

Re: [gmx-users] enegry minimisation

sonali dhindwal wrote: Hello Gaurav, when i did g_rms with structre before energy minimisation as refrence and strucutre after energy minimisation, it came to be around 0.02. Is that backbone RMSD or does it consider all protein atoms? In either case, a value of 0.02 indicates a very

Re: [gmx-users] enegry minimisation

sonali dhindwal wrote: Thanks for your reply Justin, this is rms for protein backbone, it is showing as 0.02 but when i check it in pymol by aligning two molecules rms is 0.256, and there is change in the structre of the protein. Sounds like that's the same result (potentially). Gromacs

[gmx-users] PCA

I have a little concept problem regarding principal component analysis. So my question is about ED sampling are as follows: 1. I have read from the manual that g_covar calculates and diagonalize the (mass-weighted) covariance matrix. So what is the meaning of mass-weighted in covariance matrix?

[gmx-users] graphite and pi density

Hello, I want to put charge (as pi density) on each carbon atom at 1 A top and below of each carbon atom of graphaite sheet. Basically I want put a atom, X, with charge -0.5 and mass 0 at 0.5 A below and above the carbon atom. How can I do this? Thanks Nilesh -- gmx-users mailing

[gmx-users] RE: g_densmap

Dear Mark I used this sequence to obtain the gro file (gro reference in the next calculations) g_densmap_d -f tmp-prueba.gro -n index.ndx -o tmp_prueba1.gro -princ Select a group for determining the system size: Group 0 ( System) has 6370 elements Group 1 ( HEME)

[gmx-users] Re: graphite and pi density

I want to put charge (as pi density) on each carbon atom at 1 A top and below of each carbon atom of graphaite sheet. Basically I want put a atom, X, with charge -0.5 and mass 0 at 0.5 A  below and above the carbon atom. How can I do this? Thanks Nilesh Hi Nilesh, Looks interesting. How

[gmx-users] mdrun segmentation fault

Hi I have gromacs input files for md simulation, with these set up files (*.mdp,*.top,*.itp *.gro), I can successfully run grompp and mdrun on one machine, but when I move it to other machine, I get segmentation fault when I do mdrun. Both the machines have exactly same types of installation of

Re: [gmx-users] mdrun segmentation fault

Sikandar Mashayak wrote: Hi I have gromacs input files for md simulation, with these set up files (*.mdp,*.top,*.itp *.gro), I can successfully run grompp and mdrun on one machine, but when I move it to other machine, I get segmentation fault when I do mdrun. Both the machines have exactly

Re: [gmx-users] mdrun segmentation fault

It happens immediately at step 0., and the log file looks like : Input Parameters: integrator = md nsteps = 2 init_step= 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 0

Re: [gmx-users] mdrun segmentation fault

Sikandar Mashayak wrote: It happens immediately at step 0., and the log file looks like : That suggests to me that the system is inherently unstable, which can occur for a variety of reasons. http://www.gromacs.org/Documentation/Terminology/Blowing_Up A few more comments below.

[gmx-users] polymer simulation

Dear all, I would like to know that is there any gromacs tool which can generate a polymer melt? If not, is there any tool you can suggest which can do the job. Thank you. Sudip -- ** Dr. Sudip Roy

Re: [gmx-users] confusion about segmentation fault during mdrun

Hi Justin, I took all your suggestions. But the same thing happened again in the NPT step with the Segmentation fault for some starting structure. I attached the mdp file I used. Do you have any idea what else could cause this error? Thank you very much! Best, Lan On Wed, May 19, 2010

Re: [gmx-users] confusion about segmentation fault during mdrun

Lan Hua wrote: Hi Justin, I took all your suggestions. But the same thing happened again in the NPT step with the Segmentation fault for some starting structure. I attached the mdp file I used. Do you have any idea what else could cause this error? Thank you very much! The

RE: [gmx-users] polymer simulation

If you are referring to something that will generate a coordinate file (.pdb or .gro) of polymer molecules randomly distributed, then there is not currently a script with GROMACS that will do that job. If you have a single molecule, there are a couple of tools that can randomly spread those

[gmx-users] g_bundle issue

Hi ALL, I tried to calculate the helix tilt of a single helix (TM5) among 7 helices using g_bundle. In the index file I defined the two groups (top bottom) as the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in the bun_tilt.xvg file I am getting the values as:

Re: [gmx-users] enegry minimisation

hello Jusitn, Thanks for your reply,, I am sending you the link, so that you can see the changes in the protein, I have specifically shown that part of the protein, where I am seeing changes, http://picasaweb.google.co.in/sonali11dhindwal/Protein?feat=directlink Yello beeta sheets are of the