[gmx-users] installation_server machine_error

h as below--- I got error [kashif@Server protein]$ /opt/apps/gromacs/4.6.6/bin/gmx pdb2gmx -f 1aki.pdb -o 1AKI_processed.gro -water spce -bash: /opt/apps/gromacs/4.6.6/bin/gmx: No such file or directory [kashif@Server protein]$ /opt/apps/gromacs/4.6.6/bin/pdb2gmx -f 1aki.pdb -o 1AKI_processed.

Re: [gmx-users] Atom type CB ERROR

1.85 regards kashif On Mon, May 29, 2017 at 2:36 PM, Kashif <kashifzamir180...@gmail.com> wrote: > dear sir > > I prepared ligand topology and coordinate file using swiss param tool. > Then I simulate my protein with CHARMM FORCE FILED. After giving command > > grom

[gmx-users] Atom type CB ERROR

this error. regards kashif -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman

[gmx-users] em and nvt problem

to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. kindly help regards kashif -- Gromacs Users mailing list

[gmx-users] Check stability of complex

Hi I have simulated my protein drug complex for 20 ns. My protein size was actually 600 amino acid residues but I have simulated only docked portion of my protein which was only about 300 aa residues. Now I want to see the effect of rest of my protein sequences on the stability of this 300 aa+drug

Re: [gmx-users] md continuation

. regards kashif On Wed, May 17, 2017 at 3:22 PM, Kashif <kashifzamir180...@gmail.com> wrote: > I have already run my 20 ns md simulation of my protein. The log file is > showing completion of my 20 ns data. I have also done analysis by using > trjconv command and g_rms. > Now I w

[gmx-users] Domain decomposition error

/Errors ... Although, same parameters in mdp files fairly simulated the other drug-protein complex. But this drug complex is creating trouble. kindly help. regards kashif -- Gromacs Users mailing list * Please search

[gmx-users] md continuation

t (s)Wall t (s)(%) Time: 25.0002.843 879.2 (ns/day)(hour/ns) Performance:0.061 394.912 Finished mdrun on node 0 Sat Apr 29 11:46:36 2017 regards kashif -- Gromacs Users mailing list * Please search the archive

[gmx-users] Fwd: Domain decomposition error

though, same parameters in mdp files fairly simulated the other drug-protein complex. But this drug complex is creating trouble. kindly help. regards kashif <http://www.gromacs.org/Documentation/Errors> > > -- Gromacs Users mailing list * Please search the archive at http://www.g

[gmx-users] Protein+ligand complex

run. Which parameter should be changed if there is any problem. What are the post-simulation analysis commands used for the analysis for protein+drug complex? regards Kashif -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

[gmx-users] Protein comparison

Dear all I have protein pdb file and protein+ligand pdb file generated after docking. How can I compare them by using gromacs? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Protein comparison

? Kindly suggest any tutorial for help. Thanks On Sun, Nov 16, 2014 at 3:13 PM, md kashif kashifzamir180...@gmail.com wrote: Dear all I have protein pdb file and protein+ligand pdb file generated after docking. How can I compare them by using gromacs? Thanks -- Gromacs Users mailing list

Re: [gmx-users] Ligand interaction

Dear all The protein+ligand complex energy is -1.05e+06 and energy of protein only(without docking) is -1.5...e+06, what does it mean? On Wed, Nov 12, 2014 at 9:57 AM, md kashif kashifzamir180...@gmail.com wrote: Hello everyone please suggest me that is there any change in protein energy

[gmx-users] energy minimization

Dear all Can anyone suggest that how to compare change in energy of my protein before docking and after docking by a ligand. Please suggest any suitable tutorial or paper if possible. Thanks -- Gromacs Users mailing list * Please search the archive at

[gmx-users] energy minimization of protein taken from PDB

Dear Dr. Justin Lemkul Thanks for your kind suggestion, I have energy minimized my protein taken from PDB. It gives result as -1.5248922e+06. Taking the energy minimized protein generated in .gro file file and docking it with ligand and doining energy minimization again, it gives result as

[gmx-users] Ligand interaction

Hello everyone please suggest me that is there any change in protein energy after docking the ligand to my energy minimized protein? my protein energy is -1.5e+06 and now after docking with ligand it becomes -1.05e+06. what does it mean? Thanks -- Gromacs Users mailing list * Please

[gmx-users] energy minimization of protein taken from PDB

Dear all I have downloaded a protein from RCSB, having two chains. In order to go for energy minimization should I delete one chain as both are similar and other molecules like SO4, water etc? Is the protein having chain A only can be used for energy minimization using tutorial