Re: [gmx-users] Missing Residues are list ind pdb file

Hi Jack, On Fri, Jan 15, 2010 at 8:05 PM, Jack Shultz j...@drugdiscoveryathome.com wrote: I'm trying to prep Fe-Hydrogenase again (1YQW). I took out all the non-standard residues. Re-named n-terminal and c-terminal residues. Took out connects because that worked last time though I'm uncertain

Re: [gmx-users] The size of the domain decomposition grid (1) does not match the number of nodes (8).

Hi Chris, Don't have an answer too this one, but noticed the argument to the -np option -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') Maybe it's a bit easier on the eye to use: -np $(sed -n $= $PBS_NODEFILE) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal

[gmx-users] dynamic cross correlation map (DCCM)

Hi I want to obtain dynamic cross correlation map (DCCM). I used following command for obtaining covariance matrix. g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l covar.log -xpm covar.xpm. my system consists protein of 70 aminoacids. I want survey correlated and

[gmx-users] x2top(4.0.7)

Hi all, What can be the reason that x2top(4.0.7) stops with Looking whether force field files exist Opening library file /root/gromacs.407/share/gromacs/top/ffG53a6.rtp Opening library file /root/gromacs.407/share/gromacs/top/ffG53a6.n2t Opening library file

[gmx-users] Fwd: x2top(4.0.7). More.

And more. What is the algorithm to detect that the proper atom group? Is it based both on the atom names in PDB and interatomic distances? So if we have for example Oopls_236-0.5 15.9994 1C 0.123 and in the submitted structure r(C-O)=0.126 - what it be recognized? Thanks in

Re: [gmx-users] Fwd: x2top(4.0.7). More.

Vitaly V. Chaban wrote: And more. What is the algorithm to detect that the proper atom group? Is it based both on the atom names in PDB and interatomic distances? So if we have for example Oopls_236-0.5 15.9994 1C 0.123 and in the submitted structure r(C-O)=0.126 - what it be

Re: [gmx-users] Fwd: x2top(4.0.7). More.

Justin, Thanks. The problem was that I didn't use -nopbc option. Vitaly On Sun, Jan 17, 2010 at 7:11 PM, Justin A. Lemkul jalem...@vt.edu wrote: Vitaly V. Chaban wrote: And more. What is the algorithm to detect that the proper atom group? Is it based both on the atom names in PDB and

[gmx-users] Ligand Binding to Homodimeric Proteins

Hi All, I am performing molecular docking simulations of a ligand binding to a homodimeric protein, to determine potential binding site(s). Due to the symmetrical nature of a homodimer, I would expect that the binding site(s) on one protomer would be identical on the other protomer. Therefore,

Re: [gmx-users] Ligand Binding to Homodimeric Proteins

Nancy wrote: Hi All, I am performing molecular docking simulations of a ligand binding to a homodimeric protein, to determine potential binding site(s). Due to the symmetrical nature of a homodimer, I would expect that the binding site(s) on one protomer would be identical on the other