[gmx-users] Average pdb coordinates

Dear Friends To get coordinates at specific ps i used to use following command trjconv -f md.xtc -s md.tpr -o 2000.pdb -dump 2000 *I want average pdb coordinates between 0ps to 2000ps, How i can get it ?* Regards Rituraj -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Query regarding g_rmsf and g_hbond

Dear friends, I have some query regarding g_rmsf and g_hbond 1) Through g_rmsf we can plot rmsf Vs atom number (it is by default) but i want to plot rmsf Vs time, how i can do that? 2) Through g_hbond we can plot number of H-bonds Vs Time (By default) but i want to plot number of h-bonds Vs

[gmx-users] Phosphorylation of protein

Dear friends, I want to add a phosphate (PO4) group to a amino acid residue (serine) in my protein molecule (phosphorylation of protein). Is is possible to do by in-silico (with help of Gromcs or by any other server)? Please help me in this. Thank you :) Rohan On Wed, May 19, 2010 at 7:32

[gmx-users] PCA tutorial

Dear friends, I want to do PCA for my MD data. If anybody know the tutorial regarding PCA, please let me know. Thanks in advanced Regard Rohan On 2/1/10, gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to

[gmx-users] Plot renumbering

Hello friends, As Justin replied at carla query about structure deformation after the pdb2gmx the new number retain till end. My PDB starts at 24 to 200 aa, While running xmgrace (after complete simulation) the rmsd plot is from 1 to 176aa. I understood by previous mail that gromacs renumbered

[gmx-users] Problem in g_rms

I want get rmsd deviation between NMR structure and the simulated result, but i am getting following error in following command. g_rms -s em.tpr -f md.trr -o rsmd_Calpha.xvg WARNING: topology has 50772 atoms, whereas trajectory has 22899 ---

[gmx-users] position restrained dynamics protein size

* -- -- RITURAJ PUROHIT Assistant Professor, Bioinformatics Division School of Bio-sciences and Technology (SBST) Vellore Institute of Technology, University Address: SBST, VIT University, Vellore-632014,Tamilnadu, India. Phone: +91-416

[gmx-users] Re: Regarding g_rmsf

search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 68, Issue 77 * -- -- RITURAJ PUROHIT Assistant Professor

[gmx-users] Re: xmgrace plot

* -- -- RITURAJ PUROHIT Assistant Professor, Bioinformatics Division School of Bio-sciences and Technology (SBST) Vellore Institute of Technology, University Address: SBST

[gmx-users] RMSD Vs Residue no by Grace

Dear friends, I am able to plot, RMSD between Time (ps) by following command by using GRACE.. g_rms -s md.tpr -f md.xtc xmgrace rmsd.xvg How we can I plot a graph betwwen RMSD and residue no ..?? My aim is to find RMSD at each residues. How i can do that? looking forward for u r important

[gmx-users] How to neutralize net charge of protein and why

! End of gmx-users Digest, Vol 64, Issue 198 ** -- -- RITURAJ PUROHIT Assistant Professor, Bioinformatics Division School of Bio-sciences and Technology (SBST

[gmx-users] DSSP problem

Dear all I want ti install DSSP for visualization of secondary structure in gromacs analysis. I am doing following procedure.. Copy the executable dsspcmbi to /usr/bin or /usr/local/bin ln -s dsspcmbi dssp And running it for my Pdb like that dssp file.pdb file.dssp BUt I am getting error

[gmx-users] DSSP problem

the PRODRG charges (Mark Abraham) 5. how to include ionic strength (amri ta) 6. Re: how to include ionic strength (Mark Abraham) 7. DSSP problem (rituraj purohit) 8. Re: DSSP problem (Mark Abraham) -- Message

[gmx-users] Gromacs output analysis

Hello to everybody I need the gromacs analysis document. I mean i want to do analysis (like; RMSD, traj)of my result which I got after simulation of protein molecule. If anybody having any PDF or web link emphasis the analysis part, please forword me... Thank you Rituraj On Wed, Jun 3, 2009 at

[gmx-users] Problem in fianl step of MD

Hi .. I am using gromacs 4.0 for simulating a protein molecule. i am getting following problem during md run[md.mdp dt =0.002 ; ps ! nsteps = 10 ; total 200.0 ps ] t = 47.530 ps: Water molecule starting at atom 46763 can not be settled. Check for bad contacts and/or reduce the timestep.