Re: [gmx-users] Ligand Parameters

Quoting Justin Lemkul [EMAIL PROTECTED]: I am interested in simulating some small molecules that involve oxygen in aromatic rings (which thus bears a +1 charge). I tried to submit one of these molecules to PRODRG, but got an error indicating that there were too many bonds to O. I

[gmx-users] Call for abstracts: Molecular Docking, Complexity, and Optimization. An ECCS 2007 Satellite Conference.

Molecular Docking, Complexity, and Optimization An ECCS 2007 Satellite Conference, Dresden, Germany 4th or 5th October 2007 http://pacosy.informatik.uni-leipzig.de/MDCO-2007 organised by Carsten Baldauf, Structural Bioinformatics Group, TU Dresden Daniel Merkle, Parallel and Complex Systems

[gmx-users] question about g_rmsdist

Dear all, I would like to have some elucidation about g_rmsdist output. Optionally, it outputs three matrices with the options -rms, -mean and - scl. Questions are: 1) Exploring .xpm files, I see there is a letter code which converts color exa-codes to letters to values. The resolution is

[gmx-users] new default value for emtol with gromacs 3.3???

Dear gromacs developers and users, I sent a message several weeks ago and have had no response. I am unsure if this means it is a silly question or that no-one had an answer or just that no-one got around to replying. It is with great trepidation I send this again! ;-) 1. I notice that the

Re: [gmx-users] new default value for emtol with gromacs 3.3???

Jennifer Rendell wrote: Dear gromacs developers and users, I sent a message several weeks ago and have had no response. I am unsure if this means it is a silly question or that no-one had an answer or just that no-one got around to replying. It is with great trepidation I send this again!

Re: [gmx-users] new default value for emtol with gromacs 3.3???

Hi, The default value is just set reasonably high so we avoid lots of mailing list questions about the message that energy minimization finished without converging to the requested precision. For MD it doesn't matter much at all, and for NMA you should set it to 0 and run double

[gmx-users] lipid solvent

Dear Gromacs users, I am trying to simulate a protein in a box of triglycerides TG (not in a membrane) with only a few water molecules. I have allready build the topology file for the lipid. to obtain this system I have run 3 simulations (with position restraints on protein) with triclinic

Re: [gmx-users] error estimates of free energy calculations

Hi David and Berk, Thanks a lot for all of your suggestions, which I used to take another look at my protocol. And I think I've found the main source of my problem: Starting with a file containing three columns (for lambda, dG/dl, and the error in dG/dl calculated by g_analyze -ee), I ran

[gmx-users] lipid solvent

I don't really understand what you are trying to do, but one thing that popped to mind is that if your current system is current.gro you can do this: genbox -cp empty_file_with_box_dimensions_I_want.gro -cs current.gro Basically you are solvating an empty box with replicas of your system.

[gmx-users] Calculating energies of amino acids in a protein using g_energy

Hi, I have to calculate the energy of each amino acid in the protein. In one of the questions in mailing list http://www.gromacs.org/pipermail/gmx-users/2001-November/000222.html I came across this and this is what exactly what i should do. Can you please explain that in a more clear way as

[gmx-users] amb2gmx code

Hi David, I checked the mailing list about conversion of Amber 8 or 9 topologies to gromacs topology using in house amb2gmx code. I would be really greatful if you can send me the code. Thanks, Rahul ___ gmx-users mailing list

Re: [gmx-users] amb2gmx code

http://www.alchemistry.org/FreeEnergyTools On 5/15/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi David, I checked the mailing list about conversion of Amber 8 or 9 topologies to gromacs topology using in house amb2gmx code. I would be really greatful if you can send me the code. Thanks,

Re: [gmx-users] Calculating energies of amino acids in a protein using g_energy

abhigna polavarapu wrote: Hi, I have to calculate the energy of each amino acid in the protein. In one of the questions in mailing list http://www.gromacs.org/pipermail/gmx-users/2001-November/000222.html http://www.gromacs.org/pipermail/gmx-users/2001-November/000222.html I came across

Re: [gmx-users] error estimates of free energy calculations

Jeroen, However, in my opinion (assuming the total error should be calculated from standard error propagation), the way g_analyze calculates the total error is incorrect. It results in an overestimation of this total error by at least a factor of sqrt((number of lambda points) - 1). This factor

Re: [gmx-users] Ligand Parameters

Thanks to all for sharing thoughts. I will keep the list apprised of any successes; it may be useful to others down the road. -Justin Quoting FyD [EMAIL PROTECTED]: Quoting Justin Lemkul [EMAIL PROTECTED]: I am interested in simulating some small molecules that involve oxygen in aromatic

[gmx-users] PBC problem

Hi all, We found some problems in using g_dist or g_minidist to calculate distance in some PBC condition, dodecahedron The output is as followed: Back Off! I just backed up mindist.xvg to ./#mindist.xvg.2# Warning: Triclinic box is too skewed. Box (3x3): Box[0]={

[gmx-users] Calculating energies of peptides in protein uisng g_energy

Hi Mark, I am not getting that error before with unmodified .mdp file. Abhigna ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search

Re: [gmx-users] Calculating energies of peptides in protein uisng g_energy

abhigna polavarapu wrote: Hi Mark, I am not getting that error before with unmodified .mdp file. Abhigna Well, use diff on your before and after .mdp file, because if you've only modified energygrps then I don't think this error can be occurring. Mark

Re: [gmx-users] lipid solvent

Hi SEB, The lipids aggregated and surround the protein (as expected) but asymetricaly in the box. What do you mean with this? Did you consider PBC? Try centering your system using the protein for the center of mass. I have selected only the lipids from the last run at a maximum distance of

RE: [gmx-users] PBC problem

Thanks Tsjerk, Probably because we use pressure coupling and the box size is deformed. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856

Re: [gmx-users] error estimates of free energy calculations

David Mobley wrote: Jeroen, However, in my opinion (assuming the total error should be calculated from standard error propagation), the way g_analyze calculates the total error is incorrect. It results in an overestimation of this total error by at least a factor of sqrt((number of lambda

Re: [gmx-users] error estimates of free energy calculations

David van der Spoel wrote: Will do. Of course this is why you get the source code so you can check it. Try that with excel. And actually the source code says that what you are getting is the standard deviation rather than the standard error. It should have been in the documentation of course.

Re: [gmx-users] error estimates of free energy calculations

From: David Mobley [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] error estimates of free energy calculations Date: Tue, 15 May 2007 15:55:01 -0700 Jeroen, However, in

Re: [gmx-users] error estimates of free energy calculations

From: Berk Hess [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: Re: [gmx-users] error estimates of free energy calculations Date: Wed, 16 May 2007 07:47:18 +0200 From: David Mobley [EMAIL PROTECTED] Reply-To: