Re: [gmx-users] gmx pdb2gmx for synthetic nucleic acid sequences

On 3/12/16 6:55 PM, fulvio ciriaco wrote: Hello, I have to simulate some non natural sequences containing sometimes both T and U nucleic acids. However pdb2gmx incorrectly detects the terminus, i.e., for a sequence like TCAUA it says Identified residue DT1 as a starting terminus. Warning:

Re: [gmx-users] zero free energy of ligand in water

On 3/12/16 3:43 AM, Sana Saeed wrote: hi i have performed simple ligand only simulation (part of protein ligand binding free energy calcultaion: alchemical pathway: from complex protein and ligand simulation i got 11.43 kj/mol of delta G by using gmx bar, same result i got by using

Re: [gmx-users] problem in editing .eps file of hbond

On 3/12/16 5:44 AM, tasneem kausar wrote: Dear all I have plotted the hydrogen bonds present at the interface of protein in its binary complex. I have already written the index file for the interface residues then used it for hydrogen bond calculation. There are a number of bonds at the

Re: [gmx-users] Addendum to Question

On 3/12/16 11:51 AM, Robert Molt wrote: Thank you for clarifying the proper way to search the forums. I was perhaps unclear in what I wrote. I already *have *the converted topology and trajectory files (via Parmed). Rather, I am seeking the correct command to combine them into a binary

[gmx-users] Addendum to Question

Thank you for clarifying the proper way to search the forums. I was perhaps unclear in what I wrote. I already *have *the converted topology and trajectory files (via Parmed). Rather, I am seeking the correct command to combine them into a binary (pursuant to the use of do_x3dna

Re: [gmx-users] Building Gromacs 5.1.2

Hi, If you haven't installed it, then it isn't installed. Otherwise, you're not running on the machine you think that you're running on... Mark On Sat, Mar 12, 2016 at 3:46 PM Okoroafor, Kelechi < kelechi.okoroa...@gmail.com> wrote: > Thank you very much, Mark, I greatly appreciate your

Re: [gmx-users] Building Gromacs 5.1.2

Thank you very much, Mark, I greatly appreciate your assistance. I have Ubuntu 14.0.4 live booting from an external hard drive. And if I remember correctly, before correctly completing the installation, I had tried unsuccessfully to run “mdrun” and the command was not recognized. So I highly

Re: [gmx-users] Building Gromacs 5.1.2

Hi, That just means what it says. Be aware that some distributions provide GROMACS packages, which it sounds like you might have. Mark On Sat, Mar 12, 2016 at 1:28 PM Okoroafor, Kelechi < kelechi.okoroa...@gmail.com> wrote: > Hello, > > I attempted installing Gromacs 5.1.2 with gpu enabled on

Re: [gmx-users] Query regarding energy minimization step (step 12: Water molecule starting at atom 13529 can not be settled.)

Thank you! SHRI KANT M Tech (Computational Biology) Centre for Biotechnology Anna University, Chennai 600025 On Fri, Mar 11, 2016 at 6:24 PM, Justin Lemkul wrote: > > > On 3/11/16 2:50 AM, shrikant kaushik wrote: > >> Dear all gromacs users, >>

[gmx-users] Building Gromacs 5.1.2

Hello, I attempted installing Gromacs 5.1.2 with gpu enabled on a live booted Linux system, which did not have Gromacs previously installed. When I ran “mdrun -version” I saw that Gromacs 4.6.5 was installed with gpu disabled. Please has this happened to anyone else? Would any one know what

[gmx-users] Building Gromacs 5.1.2

Hello, I attempted installing Gromacs 5.1.2 with gpu enabled on a live booted Linux system, which did not have Gromacs previously installed. When I ran “mdrun -version” I saw that Gromacs 4.6.5 was installed with gpu disabled. Please has this happened to anyone else? Would any one know what

[gmx-users] problem in editing .eps file of hbond

Dear all I have plotted the hydrogen bonds present at the interface of protein in its binary complex. I have already written the index file for the interface residues then used it for hydrogen bond calculation. There are a number of bonds at the interface. I am trying to put a cut off of 50 % for

Re: [gmx-users] Optimal hardware for running Gromacs

Dear David, I think you will find answers to many of your questions in the following publication: http://onlinelibrary.wiley.com/doi/10.1002/jcc.24030/full Best, Carsten > On 12 Mar 2016, at 02:52, David Berquist wrote: > > I'm looking into building a desktop

[gmx-users] zero free energy of ligand in water

hi i have performed simple ligand only simulation (part of protein ligand binding free energy calcultaion: alchemical pathway: from complex protein and ligand simulation i got 11.43 kj/mol of delta G by using gmx bar, same result i got by using alchemical_analysis.py --> David Mobley's) but the