[gmx-users] GROMACS-CYSTEINE PROTEASES

if anyone grants me a tutorial which can help me in this. Thank you. -- *MUSYOKA THOMMAS MUTEMI** B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science (Nagasaki University)* *PhD Student-Bioinformatics (Rhodes University) *Skype ID- MUSYOKA THOMMAS MUTEMI Alternative email - thom

Re: [gmx-users] GROMACS-CYSTEINE PROTEASES

Dear Justin, Thanks so much. If get stuck i will come knocking on your door. Cheers. On Wed, Aug 21, 2013 at 10:17 PM, Justin Lemkul wrote: > > > On 8/21/13 4:00 PM, MUSYOKA THOMMAS wrote: > >> Dear users, >> I am new to GROMACS and i have just been practising with se

[gmx-users] Re: GROMACS-CYSTEINE PROTEASES

file that i can use as my starting structure for MD simulations? Thanks. On Wed, Aug 21, 2013 at 10:00 PM, MUSYOKA THOMMAS < mutemibiochemis...@gmail.com> wrote: > Dear users, > I am new to GROMACS and i have just been practising with several tutorials. > I am trying to do a mol

Re: [gmx-users] Re: GROMACS-CYSTEINE PROTEASES

tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Any one with any solution to get through this. Thank you On Thu, Aug 22, 2013 at 10:33 PM, Justin Lemkul wrote: > > > On 8/22/13 3:25 PM, MUSYOKA THOMMAS wrote: > >> Dear

Re: [gmx-users] Re: GROMACS-CYSTEINE PROTEASES

Thanks so much Justin, I really appreciate your guidance and your input in this forum. Thanks. On Sun, Aug 25, 2013 at 6:00 PM, Justin Lemkul wrote: > > > On 8/25/13 11:35 AM, MUSYOKA THOMMAS wrote: > >> Hello, >> I am trying to minimize my ligand-protein structures bu

[gmx-users] LIGAND TOPOLOGY

there help me in understanding this. Thanks in advance. <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html>-- *MUSYOKA THOMMAS MUTEMI Mob nos **+27844846540** B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science (Nagasaki Univer

[gmx-users] GaussView 4.0 and ITP adjuster

Dear Users, I am trying to run Protein-Ligand MD simulations using GROMACS. However, i seem to be lost in building correct ligand topologies. I came across an article explaining that the above mentioned softwares can be used to build a ligand topology file that can act as a guide in allocating corr

[gmx-users] Ligand Topologies

Small-Molecule Topologies, *but seems i cannot find the way, as the system crashes down during the solvating stage with an error message;* the net charge of my structure is not an integer value. * I will be glad to get any assistance. Thank you. -- *MUSYOKA THOMMAS MUTEMI Mob nos **+27844846540**

Re: [gmx-users] GaussView 4.0 and ITP adjuster

(but far not all) results. Of course, it has nothing to do with > gromacs and its topologies. > > Or, do I misunderstand you? > > > Dr. Vitaly V. Chaban > > > On Sun, Sep 8, 2013 at 1:29 PM, MUSYOKA THOMMAS < > mutemibiochemis...@gmail.com> wrote: > >

[gmx-users] Adding ligand structure information obtained from ATB into the pdb2gmx gro file (obtained using GROMACS)

Dear Users, I am using the ATB web server to build topologies of my ligands. I have tried to include the ligand UNITED ATOM STRUCTURE (generated by the ATB) into my protein gro file generated by GROMACS by copying the information in the lines starting with HETAM to the end of my protein gro file an

Re: [gmx-users] Adding ligand structure information obtained from ATB into the pdb2gmx gro file (obtained using GROMACS)

le with a .pdb suffix. Then you > can do such a pasting operation, and if you've preserved the format > correctly, proceed to use the resulting file in future GROMACS stages. > > Mark > > On Tue, Sep 10, 2013 at 11:10 AM, MUSYOKA THOMMAS > wrote: > > Dear Users, &

[gmx-users] POSITION RESTRAIN ERROR

Dear Users, I am running Protein-Ligand MD simulations. Whenever, i get to do the Position restrain run of both my protein and ligand, i get this error; Making 1D domain decomposition 4 x 1 x 1 starting mdrun 'Protein in water' 5 steps,100.0 ps. step 0 Step 8, time 0.016 (ps) LINCS WARNING

[gmx-users] Ligand breaking in to two

Dear Users, I am doing protein-ligand MD simulations. I first prepare the ligand by adding Hydrogen atoms and setting the charges using UCSF chimera. I thereafter use acpype to get the ligand's gro,itp and top files. Finally, i process the protein.PDB file and perform MD simulations. However, when

[gmx-users] pdb2gmx conversion

Dear Users, Whenever i convert a protein.pdb file using the following command (pdb2gmx -f protein.pdb -o protein.gro/pdb -water spc) and thereafter visualise the output with either vmd or pymol, i get the first amino acid residue breaking from the main chain. Would anyone help me understand why t

[gmx-users] mdrun

Dear Users, I am running MD simulations of a protein-ligand system. Sometimes when i do an mdrun, be it for the energy minimization or during the nvt and npt equillibration or the actual md run step, sometimes the output files are named in a very odd way (strange extensions) e.g em.gro.tprr or md.

Re: [gmx-users] mdrun

Dear Dr Justin, Much appreciation. You nailed it. Kind regards. On Tue, Nov 5, 2013 at 2:41 PM, Justin Lemkul wrote: > > > On 11/5/13 7:37 AM, MUSYOKA THOMMAS wrote: > >> Dear Users, >> I am running MD simulations of a protein-ligand system. Sometimes when i >>