[gmx-users] Fw:some waters in active site of receptor

Dear, there are three waters in active site of receptor,mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system. In order to avoid the three waters

Re: [gmx-users] removing number of sol

Dear Erik, I am new to Gromacs and used AMBER before, and I am exploring various options in GROMACS too. Surely I will look in to g_select. Also as I was using sed, one should include an extra space (using vi) in gro file just before residue number and then can use sed to remove like this: sed -e

[gmx-users] Semiisotropic pressure coupling problem

Dear Gromacs users, I am doing a simulation on CO2/water interface. Two separate simulations (NPT) have been done sucessfully for pure CO2 and pure water systems. Then two CO2 gro files and one water gro files were connected into one single gro files for CO2/water interface

[gmx-users] implicit solvent

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Re: [gmx-users] do_dssp

Hi, I'll try out the 2.1.0 with do_dssp and see if there's something problematic with this new version. Good thing you brought it up. Erik On Mar 1, 2013, at 6:24 PM, Miguel Ángel Mompeán García wrote: Hi Erik, Since I read in the mailing list that nobody had asked about 2.1.0, just

Re: [gmx-users] removing number of sol

If you have a pdb file instead of a gro file then e.g. pymol might be useful. Erik On Mar 2, 2013, at 2:01 PM, gromacs query wrote: Dear Erik, I am new to Gromacs and used AMBER before, and I am exploring various options in GROMACS too. Surely I will look in to g_select. Also as I was

Re: [gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093)

On 3/2/13 1:42 AM, swati rana wrote: Hi Justin, Thanks a lot, that suggestion of yours helped. I am on the equilibration step and its running but nothing is happening on the terminal its just stagnant. Is it fine because its more than 17 hrs now. Is there some problem. After running the

[gmx-users] Re:Gromacs auxillary tools ideas

Dear All, I read a paper by Van der Groot and realized some tool regarding simple paersons r values, or correlation co-efficient by different names would be a great analytical asset for macromolecular biology. Looking over the code, g:sham seems to have begun implicating such things but it

Re: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current

Hello, I run a 500ps simulation and save the trajectory each 3fs. g_current work till 498ps and later it shows -nan. Can you tell where is the problem Nilesh Hi, Now I've tested the version of g_current in 4.6 and for me it works fine. /Flo -Ursprüngliche Nachricht- Von:

[gmx-users] mpirun: cannot open .tpr file

Hi, I'm trying to test mpirun, so I tried with the NPT equilibration. From the tutorial of: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html I run this command: mpirun --np 10 --hostfile ~/hostfile mdrun_mpi -npme 3 -deffnm npt and obtained an