Re: [gmx-users] How to generate average C-alpha fluctuation during MD of every AA residue?

Shanjie Huang wrote: Hi my dear friends, I just learn to use gromacs this days and I found a lot of figures in research articles that illustrates the average C-alpha fluctuation during MD of every AA residue, which can show very clearly that which part of protein is stable and which is flexible.

[gmx-users] How to generate average C-alpha fluctuation during MD of every AA residue?

Hi my dear friends, I just learn to use gromacs this days and I found a lot of figures in research articles that illustrates the average C-alpha fluctuation during MD of every AA residue, which can show very clearly that which part of protein is stable and which is flexible. But I examined the tut

Re: [gmx-users] bugzilla

David Mobley wrote: All, I can't connect to bugzilla.gromacs.org currently. Is it down? works for me. can someone confirm that it works from off-site as well? Thanks, David ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

Re: [gmx-users] Ligand moves out of box during EM steps

Thanks for all your suggestions, But according to David mobley, I tried but no effect, the ligand still found at the corner with its atoms are in distorted condition. I use these commands : >pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh Where protein with its ligand cut off. later I

RE: [gmx-users] g_hbond question

try g_hbond -g! daniela On Wed, 2006-03-22 at 06:15 -0600, Moore, Jonathan (J) wrote: > Daniela, > > Thanks for that tip. It looks like that won't help me, though, because I > can't get it to write out the log file. > > Jonathan > > > Jonathan Moore, Ph.D. > Rese

[gmx-users] bugzilla

All, I can't connect to bugzilla.gromacs.org currently. Is it down? Thanks, David ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www int

Re: [gmx-users] ns_type=grid leads to blowups in minimization but not with ns_type=simple

David, > If there's no bugzilla there isn't a bug. Please upload two tpr files > with the only difference being the NS type that sow the mentioned behavior. I will upload to bugzilla. I know there isn't an *existing* bug: I was asking whether this was expected behavior (that is, if I should even

Re: [gmx-users] mdrun -rerun with gmx3.2 and gmx3.3

David, My conclusion so far is that trr file must be used for rerun (we learn every day, isn't it fabulous !) and I do not see the bug you pointed out but probably due to the system I run !! Well, that sounds like good news. If we accept to not understand why you got a different result,

Re: [gmx-users] ns_type=grid leads to blowups in minimization but not with ns_type=simple

David Mobley wrote: Dear all, I've been having some very sporadic problems with minimization (that is, only on some of the many systems I minimize). In some cases, during steepest descent minimization (following L-BFGS, which essentially ends immediately for the system in question), minimization

Re: [gmx-users] mdrun -rerun with gmx3.2 and gmx3.3

Xavier, > My conclusion so far is that trr file must be used for rerun (we learn > every day, isn't it fabulous !) > and I do not see the bug you pointed out but probably due to the system > I run !! Well, that sounds like good news. I am not surprised that the reduced precision trajectories giv

Re: [gmx-users] Fw: TM protein, lipids, force field

Shalom, In the lab I work in, we use DMPC and the GROMOS87 ff (see Tieleman site). I saw that POPC is represented in the new ff (GROMOS96), so you might try it, or build your top file using the atoms found at the ff files (as lego). Best, Itamar. Quoting P <[EMAIL PROTECTED]>: > > > > Dear Gro

Re: [gmx-users] mdrun -rerun with gmx3.2 and gmx3.3

David, I'll try to explain a bit better and I attached a gziped pdf file containing a reduced set of energies that I sent at my first post. I, too, am slightly confused about what exactly the differences are you're seeing. Could you perhaps make a little table or something? Partly, I just do

[gmx-users] ns_type=grid leads to blowups in minimization but not with ns_type=simple

Dear all, I've been having some very sporadic problems with minimization (that is, only on some of the many systems I minimize). In some cases, during steepest descent minimization (following L-BFGS, which essentially ends immediately for the system in question), minimization runs for about 10 ste

[gmx-users] Fw: TM protein, lipids, force field

  Dear Gromacs Users.I’m new gromacs user and I would be glad to get some advice from you.I wan to do MD of TM-protein in DPPC lipid bilayer and then I would like to investigate interactions between this protein and the ions present in the system.  I’ve read the manual and checked mailing l

Re: [gmx-users] Ligand moves out of box during EM steps

If I remember correctly, the place where the coordinates of the protein get changed is the step involving genbox (or editconf), where it is translated to the center of the box. So an alternative approach to Alberto's suggestion is to combine the protein and the ligand *before* using editconf/genbox

Re: [gmx-users] ffG43a1.n2t

Marco Deriu wrote: Dear all, I ran x2top (gromacs 3.3) command to get DNA.top file from DNA.gro. But it gave me error for all the forcefields I used. The error was as follows: Fatal error: Library file ffG43a1.n2t not found in current dir nor in default directories. Also when I used other force

[gmx-users] ffG43a1.n2t

Dear all,I ran x2top (gromacs 3.3) command to get DNA.top file from DNA.gro. But it gave me error for all the forcefields I used. The error was as follows:Fatal error: Library file ffG43a1.n2t not found in current dir nor in default directories.Also when I used other forcefields it gave me s

Re: [gmx-users] Ligand moves out of box during EM steps

Hi Raja,I meant your "ligand"  or "ligands first atom". Sorry for the confusion there.TsjerkOn 3/22/06, Alberto Malvezzi <[EMAIL PROTECTED]> wrote:Hi Nataraj, this happened to me also.When you make an energy minimization, gromacs alters the coordinates ofyour protein. When you place the ligand bac

Re: [gmx-users] Ligand moves out of box during EM steps

Hi Nataraj, this happened to me also. When you make an energy minimization, gromacs alters the coordinates of your protein. When you place the ligand back to the gro file, it will be placed far from its site. To solve this problem I take the original complex and fit it to the minimized protein

Re: [gmx-users] Req for script to make rtp entro of ligand with ffoplsa compatiable

Hi Raja, an entry for a molecule in the rtp database you have to create on your own - the principles how to "explain" your ligand to Gromacs is simple, just take a look onto the aminoacids in there and how they are described. Will take you some time (roughly some days probably), but it will wo

[gmx-users] Req for script to make rtp entro of ligand with ffoplsa compatiable

Dear GMXIONS, Kindly provide me a script to make rtp entry for a ligand to use it for oplsa force field file. With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Access your email from home and the web ___

Re: [gmx-users] Ligand moves out of box during EM steps

Dear Tsjerk, Thanks for your prompt replies, But please bit elaborate your answer. Yea I do use editconf for the purpose of renumbering ligand after pasted in original protein gro file produed by pdb2gmx step (as per my previous mail). But where come the option of -s in ediconf

Re: [gmx-users] Ligand moves out of box during EM steps

Hi Raja,When you generate a .tpr file (for whatever purpose) all molecules will be mapped to a rectangular box as good as possible. For this, the first atom of the molecule is used. So when a molecule happens to be sticking out of the rectangular box, or when it is just pushed over the border durin

Re: [gmx-users] Ligand moves out of box during EM steps

Dear Tsjerk, Thanks for your reply. But I have not gone to the stage of dynamics yet. I am still struck at energy minimization. Now atleast I could reason out why it happens, but I dont know how to stop it. The reason is everytime when I convert ligand-enzyme comple

RE: [gmx-users] g_hbond question

Daniela, Thanks for that tip. It looks like that won't help me, though, because I can't get it to write out the log file. Jonathan Jonathan Moore, Ph.D. Research and Engineering Sciences - New Products Core R&D The Dow Chemical Company 1702 Building, Office 4E Midl

[gmx-users] Re:Re: Re: Re:double precision minimization with version 3.3

>Message: 1 >Date: Tue, 21 Mar 2006 18:44:25 +0100 >From: Florian Haberl <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Re: Re:double precision minimization with > version 3.3 >To: Discussion list for GROMACS users >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="utf-8" >

[gmx-users] Re: position of a molecule in a bilayer

Hi Rama, It sounds to me that the best prog. to use will be "g_density". This useful programme calculates partial densities of system components. You can then deduce the position of a small molecule inside a lipid bilayer by computing partial densities of the lipids, small molecule and solvent (sp

Re: [gmx-users] gromacs manual

Itamar Kass wrote: Shalom all, I also wish to get a copy, and I guess that this is true for other. So whay not to put a copy on the Gromacs's site? It's broken, but I'll fix it *Real Soon Now* Itamar. Quoting Anthony Cruz <[EMAIL PROTECTED]>: Hi: I have been trying to make the manual fro

Re: [gmx-users] pdb2gmx illegal instruction

Dongsheng Zhang wrote: Dear Erik, Thank you very much for your reply. I have fixed the problem with David's helps. Now I am struggling with parallel running with gromacs. I use grompp -np 8 -sort -shuffle -f pr -o pr -c after_em -p AceAla5ac to get pr.tpr When I submitted a job to the comput