[gmx-users] gmx_clusterByFeatures - Features Based Conformational Clustering of MD trajectories

examples. Feedback are welcome. Thanks and regards, Rajendra -- |==| |* Dr. Rajendra Kumar *| | Post-Doctoral Researcher | | Department of Chemistry | | Umeå University <http://www.umu.se/english/>, | | Umeå,

Re: [gmx-users] Groove width

On Mon, Jun 4, 2018 at 1:10 PM, wrote: > Hii >> I have tried installation of do_x3dna in ubuntu system following the >> instructions given in the link. Installation done successfully then I >> have written the path of do_x3dna in .bashrc file(export >> do_x3dna=/usr/local/do_x3dna/bin/) and

Re: [gmx-users] Groove width

> > > I am doing simulation of DNA molecule. I want to calculate groove width of > DNA in GROMACS. How to do this? Someone please help. > > ​You may use do_x3dna (http://do-x3dna.readthedocs.io). It uses 3DNA in background and works with GROMACS files.​ Package also includes tools to analyze the

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

Hi, As suggested above, use -ignh to ignore hydrogen atoms. To use a specific Histidine, you may change residue name HIS to HIP(Amber)/HSP(Charmm)/HISH( ​OPLS​ ) or HID(Amber)/HSD(Charmm)/HISD( ​OPLS​ ) or HIE(Amber)/HSE(Charmm)/HISE( ​OPLS​ ) either in PDB file or interactively through pdb2gmx

Re: [gmx-users] Query on g_mmpbsa in gromacs

Pairwise interaction scheme ​ is not implemented in g_mmpbsa. Therefore, g_mmpbsa cannot be used to calculate interaction energy between two residues. With best regards, ​Rajendra ​ On Mon, Mar 28, 2016 at 2:37 PM, Prasanna Dr wrote: > Hi > > I have been using

Re: [gmx-users] g_mmpbsa positive binding energy

Hi, MM/PBSA method has several limitations (discussed in several publications) and therefore, you may be getting positive energy values from these limitations. You may get a negative binding energy after further increasing the dielectric constant, however, interpretation of this value would be

Re: [gmx-users] g_mmpbsa time

You may use -dt as option in g_mmpbsa. For example, -dt 600 or -dt 120 . On Thursday, September 17, 2015 at 7:41:25 AM UTC+2, elham wrote: > > Dear users > i simulated a system for 30 nano-seconds(dt=2fs) and my frame was 6 ps > for binding free energy computations by g_mmpbsa method in gromacs,

Re: [gmx-users] Force field For Protein-Ligand Complex

You may also use Amber99sb-ildn and GAFF for protein and ligand, respectively. You can find method in this paper: http://pubs.acs.org/doi/full/10.1021/ci500020m. Although, AM1-BCC method was used for charge calculations, I would suggest to use RESP method. With best regards, Rajendra -- Gromacs

[gmx-users] g_distMat: A tool to calculate average min-distance matrix on multiple CPU cores

Dear GROMACS Users, I have wrote a small tool g_distMat (https://github.com/rjdkmr/g_distMat). It is almost similar to the g_mdmat. Features: Average minimum-distance matrix (residue-wise) between two index groups Related Standard deviation and variance matrix Fraction of Contacts(map) over