[gmx-users] antigen-antibody insilico MD using GROMACS

Hi Gromacs users, I am studying antigen-antibody interaction at protein level. I have a protein sequence (no crystal structure, length 180 residues) of the antigen, and have predicted the secondary structure of it (and modeled). By performing conserved domain search using inferno and NCBI I found

[gmx-users] New files after simulation run

Hi All, I have run an extended simulation for 90ns like this: (my previous run was for 10ns) grompp -f new.mdp -c old.tpr -o new.tpr mdrun -s new.tpr -cpi old.cpt I output mdrun STDOUT to an output file and it looks like this: ## Back Off! I just

[gmx-users] Fwd: extended calculation pdb extracttion query

Dear ALL, I have run an extended simulation for 90ns like this: (my previous run was for 10ns) grompp -f new.mdp -c old.tpr -o new.tpr mdrun -s new.tpr -cpi old.cpt because, I had to make changes in the .mdp file. I have got new files from the new extended run; new.tpr, new.xtc etc My

[gmx-users] extended calculation pdb extracttion query

Dear ALL, I have run an extended simulation for 90ns like this: (my previous run was for 10ns) grompp -f new.mdp -c old.tpr -o new.tpr mdrun -s new.tpr -cpi old.cpt because, I had to make changes in the .mdp file. I have got new files from the new extended run; new.tpr, new.xtc etc My

[gmx-users] extended calculation pdb extracttion query

Hi All, I have run an extended simulation for 90ns like this: (my previous run was for 10ns) grompp -f new.mdp -c old.tpr -o new.tpr mdrun -s new.tpr -cpi old.cpt because, I had to make changes in the .mdp file. I have got new files from the new extended run; new.tpr, new.xtc etc My

[gmx-users] Fwd: Can a mutation make a protein stable - result analysis from GROMACs run

Hello All, I ran a 10ns simulation on a wild and mutant type of a protein complex. Attached is the rmsf graph. "Green" is the mutant protein with mutation at residue 71 (marked) and "purple" is the wild protein. After looking at the graph can it be said that the mutant has made the complex more

[gmx-users] Can a mutation make a protein stable - result analysis from GROMACs run

Hello All, I ran a 10ns simulation on a wild and mutant type of a protein complex. Attached is the rmsf graph. "Green" is the mutant protein with mutation at residue 71 (marked) and "purple" is the wild protein. After looking at the graph can it be said that the mutant has made the complex more

[gmx-users] Can a SNP mutation make a protein stable - result from GROMACs run

Hello All, I ran a 10ns simulation on a wild and mutant type of a protein complex. Attached is the rmsf graph. "Green" is the mutant protein with mutation at residue 71 (marked) and "purple" is the wild protein. After looking at the graph can it be said that the mutant has made the complex more

Re: [gmx-users] DSSP executable

Thanks Marc! On Mon, Sep 11, 2017 at 6:07 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > You're reading too far into http://swift.cmbi.ru.nl/gv/dssp/. The first > two > sentences are useful for you ;-) > > Mark > > On Mon, Sep 11, 2017 at

[gmx-users] DSSP executable

Hello All, Can someone please help me get the "dssp" executable? For secondary structure analysis. I did this: rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /path_to_dssp/ This downloaded all dssp pdb files but no executable. I am doing this because I got the error on gromacs run. Fatal error:

[gmx-users] Fwd: MD of native complex

Hello All, I have done MD of a native pdb structure 2LL7 for 10ns. Looking at the trajectories in PyMOL, I see that in the native structure one of the helix (short separate chain ID) tends to unfold. Is this possible in the simulation of native complexes? Thanks & Regards. -- Gromacs Users

[gmx-users] MD of native complex

Hello All, I have done MD of a native pdb structure 2LL7 for 10ns. Looking at the trajectories in PyMOL, I see that in the native structure one of the helix (short separate chain ID) tends to unfold. Is this possible in the simulation of native complexes? Thanks & Regards. -- Gromacs Users

Re: [gmx-users] Result analysis of protein water

Oak Ridge National Laboratory > Center for Molecular Biophysics > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Deep > kumar <deepak.choube...@gmail.com> > S

Re: [gmx-users] Result analysis of protein water

Hello All, I have performed MD on a protein water for 10ns, protein with total 164 residues in two chains. I have got the result graphs of radius of gyration and rmsd for both wild and mutant. Wanted to attach the graphs but could not due to bytes limit. There is one residue mutation (M -> T) in

Re: [gmx-users] gromacs ligand topology file for "GNP"

Hello, On Thu, Sep 7, 2017 at 1:11 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/6/17 3:46 PM, Deep kumar wrote: > >> Dear All, >> >> I have produced the "ITP" files of the ligands using ATB server. I am >> mentioning the steps here,

[gmx-users] gromacs ligand topology file for "GNP"

Dear All, I have produced the "ITP" files of the ligands using ATB server. I am mentioning the steps here, please let me know if you think anything is wrong. a) uploaded the coordinates of ligand "RND" on ATB server. I chose "heteromoelcule" molecule type. b) Entered the "net charge" by

Re: [gmx-users] Gromacs error: equilibration phase

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html) says, I have to prepare a position restraint file "posre_RND.itp" from the "RND.gro" file, so how can I get the "RND.gro" file? Thanks, Deep On Tue, Sep 5, 201