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 pro

[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, a

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 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 interato

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.

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 advance

[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 /root/gromacs.407/share/gromacs/top/ff

[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 anti-correla

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 Ch

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

Hi Jack, On Fri, Jan 15, 2010 at 8:05 PM, Jack Shultz 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 if connect > really mater