[gmx-users] Error in Umbrella sampling command

Dear Sir Presently I am working with the example file as given in the umbrella sampling tutorial. While running the following command grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr I got the following error. How to debug this error. Ignoring obsolete mdp entry 't

[gmx-users] Conversion of nm to Å

Dear Sir I have to query as to how do we convert the paramaters in "nm" to Å --. For example the RMSD and RMSF calculation gives result in "nm". I want to convert it to Å. I request you to kindly guide me with the process Thanking You with Regards. Arunima Shilpi Ph

[gmx-users] application of MM-GBSA

Hello sir, I require to calculate binding energy using MM-GBSA method. I searched through the manual but i did not find any. i request you to kindly guide to as to which manual to follow to identify binding energy. Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer

[gmx-users] residue labeling in g_rmsf

Respected Sir If i want my residue name to be labeled in the graph for g_rmsf ,how should I proceed... I used the following command g_rmsf -f md_0_1.xtc -s md_0_1.tpr -res -o rmsf.xvg -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer & Epigenetics) Departmen

[gmx-users] error in running g_dist

Molecule in topology has atom numbers below and above natoms (11793). You are probably trying to use a trajectory which does not match the first 11793 atoms of the run input file. how to debug the error... -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer & Epigene

[gmx-users] residues interaction with ligand

Respected Sir If we have to find the residues surrounding the ligand in protein ligand complex... than which gromacs command should be used... Looking forward for your reply. -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer & Epigenetics) Departmen

[gmx-users] Interaction spectra of inhibitor–residue pair in the protein–inhibitor complexes

Respected sir Which command do we use to determine "Interaction spectra of inhibitor–residue pair in the protein–inhibitor complexes" as we have g_hbond to determine the hydrogen bond between protein and ligand -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scho

[gmx-users] Center of Mass (COM) spacing between protein and ligand

Regards. Arunima Shilpi Ph. D Research Scholar(Cancer & Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] system hangs while running perl distances.pl

... while when I run indivdual file for distance calculation i am able to run the command g_dist -s pull.tpr -f conf1.gro -n index.ndx -o dist1.xvg < groups.txt i request you to kindly guide me to debug the error -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Can

[gmx-users] query respect to perl distances.pl

836) which means the trajectory file does not include the ligand component how to overcome this error Regards Arunima -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer & Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha

[gmx-users] groups selection make_ndx -f npt.gro

protein and ligand. Regards Arunima -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer & Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mai

[gmx-users] error in running distances.pl

Hello Sir While running command for perl distances.pl.. system gets hanged...while processing particular group file... I will be thankful to you if you can guide me in debugging the error -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer & Epigenetics) Departmen

[gmx-users] error in running perl distance.pl

ide me in rectifying the error -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer & Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

[gmx-users] center of mass and box co-ordinates

You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer & Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] Distance of pull group 1 (2.142226 nm) is larger than 0.49 times the box size (2.184750)

the command for mdrun -s pull.tpr Have the following error "Distance of pull group 1 (2.142226 nm) is larger than 0.49 times the box size (2.184750)" I request you to kindly help me to debug the error -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer

[gmx-users] distance of pull group 1 is larger than the box size

Hello sir I got the following error while running pulling mdrun -s pull.tpr "distance of pull group 1 is larger than the box size" I request you to kindly guide me in overcoming the error -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer & Epigeneti

[gmx-users] PMF calculation between protein and ligand

Sir I have query as to how to go ahead for potential mean force (PMF) calculation between protein and ligand. As per the umbrella sampling protocol you have provided us in gromacs tutotrial it says it is for protein molecules... -- Thanking You with Regards. Arunima Shilpi Ph. D Research

[gmx-users] Re: gmx-users Digest, Vol 108, Issue 183

.@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 4/30/13 12:33 PM, lloyd riggs wrote: > > I appologise, I meant defined at the same time without complaining, not > just > > either direction. > > A different atom order is interp

[gmx-users] Re: gmx-users Digest, Vol 109, Issue 2

t; > > > > I'm not sure what this means. It seems to be implying that I don't have > a box around my polymer, but the gro file clearly shows that my box is 4.94 > x 4.94 x 4.94. Any ideas? > > > > What is your setting fo

[gmx-users] Re: gmx-users Digest, Vol 108, Issue 140

this ? > I have checked potential energy of model system (single point energy > calculations i.e., zero step MD and the one that obtained from the code > that I have written, both are matching. > I am using GROMACS version 4.5.5 and also tested the same thing in V 4.6. > > Can anybo

[gmx-users] adjust charge

Dear Sir I have query as what criteria do you follow to adjust the charges of ligand atoms in topology file (drg.itp) as you have shown in example for jz4 looking for your reply -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer & Epigenetics) Department of

[gmx-users] error in running command

Dear Sir/ Madam I am using gromacs for simulation and has the following while running the command for "grompp" Expected integer argument for option -maxwarn "".  I do not want use maxwarn to bypass the error. I request you to kindly help me out to debug the error. Regards Arunima -- gmx-users