[gmx-users] Binding free energy calculation by thermodynamic integration

Hi, I want to use thermodynamic integration for calculating free energy of binding of ligand to its receptor protein. For that I would like to follow the two step approach: first decoupling Coulombic and then vdW interactions. 1. Shall I start with the same coordinate and topology files for bot

[gmx-users] about mdrun_make_hole.tar.gz

Dear all,     I want to insert a protein (L-shaped) in lipid bilayer whose C-terminal segment remains trans-membrane with solvent exposed N-terminus. For that reason, i want to use make_hole program. I have downloaded mdrun_make_hole.tar.gz & gromacs-3.1.4.tar.gz from the new gromacs hom

[gmx-users] mdrun_make_hole installation

ult. You can find information at www.gromacs.org, or in the INSTALL file. make make: *** No targets specified and no makefile found.  Stop. Please suggest any wayout. Thanks in advance

[gmx-users] mdrun_make_hole installation

ing for ur suggestion. Moutusi Manna Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] peptide insertion in lipid bilayer

ove this problem. waiting for ur suggestion. Moutusi Manna       Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

[gmx-users] mdrun_make_hole installation

Dear Ansgar Esztermann,                     Thanks for your kind help. With fftw-2.1.5.tar.gz i can successfully install gromacs-3.1.4. With regards, Moutan>usi Manna Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com__

[gmx-users] problem during position restraint simulation

Dear all,     i want to simulate a protein solvated in water. I have downloaded the protein  coordinate from RCSB  protein data bank (ID 2KB7). These has 20 merged coordinate & i have taken conformer #6. Then i run pdb2gmx with ffG43a1 & solvate the protein with spc waters. Next i energy

[gmx-users] Z-position calculation

Dear all,     I want to calculate the vertical position (Z-axis) of different lipid head groups as a function of time.     Looking forward for any suggestion.     Thanks in advance, Moutusi Manna Yahoo! India has a new look. Take a sneak peek http

[gmx-users] % of existence of hydrogen bond

regards,   Moutusi Manna   Now, send attachments up to 25MB with Yahoo! India Mail. Learn how. http://in.overview.mail.yahoo.com/photos___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] calculation of chemical shift anisotropy

Dear all,     I have simulated a small peptide on lipid-water interface under NPT condition. Is it possible to calculate the chemical shift anisotropy of the peptide from the simulation trajectory? Moutusi Manna The INTERNET now has a personality. YOURS! See your Yahoo

[gmx-users] hi

I want to perform simulation of transmembrane peptide. I have a perseuillibrated POPO (hydrated) bilayer (using CHARMM),containing more than 32,000 atom. But when I try to convert ".pdb" to ".gro" using "pdb2gmx", it shows the following error Fatal error: Residue "popc" not found in resi

[gmx-users] problem during converting ".pdb" to ".gro"

I want to perform simulation of trans-membrane peptide. I have a equilibrated POPC (hydrated) bilayer (using CHARMM),containing more than 32,000 atom. But when I try to convert ".pdb" to ".gro" using "pdb2gmx", it shows the following error Fatal error: Residue "popc" not found in residue

[gmx-users] POPC simulation

thanks for reply.I want to perform simulation of popc membrane. Steps which i have done are as follows: 1. download popc128a.pdb, popc.it,lipids.itp (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies) 2. download ffgmx_lipids files 3.convert POPC of .top & popc.itp i

[gmx-users] POPC simulation

Hi I want to perform peptide + popc membrane simulation. I download popc128a.pdb from (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies). Before I introduce the peptide into the membrane, the water layer had to be broadened to ensure full solvation of the peptide .I i