[gmx-users] calculation of persistence length

Dear all, I want to calculate the persistence length of a single stranded DNA in the presence of various salts. I want to plot a lnP(theta) vs 1-cos(theta) graph, where theta is the bend angle of the DNA and P(theta) is the angular probability. From GROMACS what I obtained was as follo

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 137, Issue 61

Thanks Mark and Joao I'm able to make peptide bond for the Cyclic peptide using specbond.dat but there is a additional Oxygen and Hydrogen atom on the Carbon and Nitrogen atom.when i run pdb2gmx selected Amber forcefield it didnt ask for the terminals and created topology with amid bond for the c

[gmx-users] miscelle formation using ligands only

I am using gromacs for the first time . I have installed gromacs 5.0.4 version and i want to check a miscelle is formed or not using 5 different ligands in different ratios. I have gone through all basic tutorials on how to use gromacs ( lysosyme,protein-ligand). But i am stuck with the problem o

Re: [gmx-users] How to create a spherocylindrical wall

On Fri, 2015-09-11 at 11:57 +0530, Jagannath Mondal wrote: > Hi > I would like to perform a simulation ( without any periodic > boundary > condition) where I need to have a wall of spherocylindrical geometry. > In > other words the particles will be confined inside a spherocylinder. > > Is ther

Re: [gmx-users] Creating a box of water with density 1000 g/l

On 9/11/15 11:46 AM, Ebert Maximilian wrote: Thanks for the reply. I think I can simulate it now. The only thing I don’t understand and this is in reference to my other post: OPLS/AA parameters for 2-propanol How can the self-diffusion coefficient be a good measure for testing my parameters

Re: [gmx-users] Protein-ligand interaction calculation

On 9/11/15 9:46 AM, michael zhenin wrote: Hello, I have simulated (REMD simulation) a protein complexed with a ligand and wanted to know if there is any option for calculating the non bonded energies between the protein and the ligand (throughout the entire simulation). Use energygrps in th

Re: [gmx-users] g_hbond

On 9/11/15 2:43 AM, Shahid Nayeem wrote: Dear all I have used g_hbond with -hbn -hbm flag to get .ndx file and .xpm file. Then with xpm2ps I converted .xpm to .eps file. I get half the number of rows in .eps file as compared to .ndx file. when using Justins perl script I got summary of existenc

Re: [gmx-users] Cyclic peptide by using specbond.dat

Hi, Yes, that's exactly what parts of the output are saying. Mark On Fri, 11 Sep 2015 22:45 João M. Damas wrote: > This does not seem related with specbond.dat, but rather a problem with the > chains: each residue is a different chain and maybe that is causing > troubles with the termini. Remo

Re: [gmx-users] Cyclic peptide by using specbond.dat

This does not seem related with specbond.dat, but rather a problem with the chains: each residue is a different chain and maybe that is causing troubles with the termini. Remove the chain ID or make them all chain A. João On Fri, Sep 11, 2015 at 6:39 PM, Nikhil Maroli wrote: > *Dear Gromacs use

[gmx-users] Cyclic peptide by using specbond.dat

*Dear Gromacs users* *i have been having a bit of issues generating accurate topology for cyclic peptide* *i added extra terms in specbond.dat (Last Line)* *as * 9 CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 CYS SG 1 HEM FE 2 0.25 CYS2 HEME CYS SG 1 HEM CAB 1 0.18 CYS2 HEME CYS SG 1 HEM CAC 1 0.18 CYS2 H

Re: [gmx-users] gromacs-5.1 with charmm36.ff

Thanks for the quick response - that fixed my problem Krzysztof On 9/10/15 5:36 PM, Justin Lemkul wrote: On 9/10/15 6:17 PM, Krzysztof Kuczera wrote: Hi I have run into a strange problem when making an urea+tip3p water box When trying to set up an energy minimization with gromacs-5.1 I g

Re: [gmx-users] Creating a box of water with density 1000 g/l

Thanks for the reply. I think I can simulate it now. The only thing I don’t understand and this is in reference to my other post: OPLS/AA parameters for 2-propanol How can the self-diffusion coefficient be a good measure for testing my parameters if for TIP3P water the self-diffusion coefficient

[gmx-users] Protein-ligand interaction calculation

Hello, I have simulated (REMD simulation) a protein complexed with a ligand and wanted to know if there is any option for calculating the non bonded energies between the protein and the ligand (throughout the entire simulation). Thanks you in advance, Michael. -- Gromacs Users mailing list * P

[gmx-users] calculating total percentage of time from gibbs free energy landscape

Is it possible to calculate total percentage of time invested to attain a minima from Gibbs free energy landscape obtained by g_sham output, such as from gibbs.xpm? Please guide me if there is any script available to do it. Nabajyoti Goswami Bioinformatics Infrastructure Facility Department of An