[gmx-users] .rtp file

Hello, I ve a query.I ve not created .rtp file,.atp file.I ve only .pdb file and i used pdb2gmx command and successfully got .top,.itp and .gro file. Do my files contains error without making use of .rtp and .atp files.Its just a curiosity to know.And how to make .rtp and .atp files. thanx. --

[gmx-users] (no subject)

Hello, I got all confused.So i started with the beginnning.i generated topology for my protein Streptavidin and generated topology for my ligand using prodrg2.5 server. I am getting error at step editconf i.e.Fatal error:Something is wrong in the coordinate formatting of file conf.gro. Any sugge

[gmx-users] fatal error occuring.

Hello Justin, After setting up grompp command,i am getting an error "Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 1, while at->nr = 1179)".I am heading up step by step taking your aid. What should i do?How to correct it?? Thanx. ---

[gmx-users] .ppa file

Hello Justin, I am doing project on afm simulation of protein complex.I have used em.mdp file for minimization. Now i am wondering where to use .ppa file for afm parameters. Can you guide me with files related to afm simulation. - This email has been sen

[gmx-users] afm simulation

Hello, I went through the tutorial umbrella sampling and i found that it is similar to afm simulation only using harmonic potential. May be i am wrong.Can you just satisfy my curiosity? Thanx. - This email has been sent using ArithMail at "Indian Instit

[gmx-users] restraining the ligand.

Hello gmx_users, I have a query.I generated my ligand topology from swissparam using charmm forcefields.Later in the tutorial after minimization step,You have mentioned of program genrestr to restrain the ligand. Is it applicable to all other methods that are not following prodrg software.If not,

[gmx-users] pull parameters

Hello gmx_users, I want to pull ligand out of binding pocket of protein using a spring of some force constant which i will vary with each simulation and with varying pulling velocity. F=K(xspring - x ligand) using this equation.Now I am stucked up how to decide initial position of ligand and spri

[gmx-users] force vs displacement

hello Justin, For afm simulation,I have obtained force vs time and displacemnet vs time plot.how to get force vs displacement plot? please tell. Thanx - This email has been sent using ArithMail at "Indian Institute of Information Technology, Allahabad,