[gmx-users] dimer simulation

Dear gmx-users I want to simulate a protein which biological function defined by dimer formation. I need to simulate this protein in dimer as well as in monomeric form to solve my objectives. I am using Gromacs-4.0.4 for simulation. I have a doubt, is there any specific parameters for dimer simulat

[gmx-users] Targeted Molecular Dynamics Simulation

I want to simulate a comformation change of a protein from state A to B. >From reference, I know the targeted molecular dynamics developed by Prof. J. Schlitter can do such task. I have also read few papers in which people has used gromacs for TMD. I searched gmx mailing list but i did not fined su

[gmx-users] Re: grompp error- Excluding 3 bonded neighbours-Fatal error

> dear dean, there is no problem with your mdp file. for grompp number of atoms in .top file and input .gro file should be equal,look your.top file, this may be because u have added number of ions in your .top file but it not present in your .gro file( difference of 8 atom only in both file, which

[gmx-users] eigenvalues

Hi Tsjerk, thanks actually my protein is quite larg (509 aa).i had divided my trajectory in different part and according to your suggestion i calculated cosine-content for all, and find that trajectory from 5to15 ns and 18to25ns having cosine value very less about 0.03 in both cases(with and withou

[gmx-users] re : heme group

hi, heme group is not an amino acid, pdb2gmx only support the amino acids because .itp and .dat file in gromacs have only information about protein atoms not for other. so u just cut the co-ordinate of heme group from your pdb file save it in other pdb file and give input for Prodrg software it wil

[gmx-users] eigenvalues

dear gromacs users, i did PCA analysis for my trajectory using g_covar and g_anaeig, i have taken trajectory of 25ns from both protein alone and protein_withligands(i did two simulation one with ligands and other by removing the ligands from pdb file)and extracted eigenvalues along first 10 eigenv

[gmx-users] re :about converting output

Dear shirin u can get your output in .pdb format by using command trjconv or by editconf. type trjonv -h or editconf -h on your terminal for more help. sanjay upadhyay Research Scholar protein dynamics lab Dept of chemistry IIT powai, Mumbai 400076 __

[gmx-users] rmsip

thanks Tsjerk for your help. I have calculated RMSIP value and overlap matrix using g_anaeig with tag -inrp and -over. i wat to conferm that is it same a we got from script that sended by u??? can i beleive on this result or nedd to check by using script. thanks a lot sanjay _

[gmx-users] regarding :RMSIP calculation

dear groacs users I want to calculate r.m.s.i.p for exploring convergence of my system and motions of two different proteins,i divided my trajectory in two equal parts and did g_covar for getting eigenvectors and corresponding eigenvector trjectory as trr file for C-alpha atom of 10 eigenvectors.

[gmx-users] chirality check

dear gromacs user, i am doing simlation of a small molecules which have chiral corbon. i want to chechk whethere the chirality maintaned during simulation or not, any one sugest me how to check it. thanks sanjay ___ gmx-users mailing listgmx-users@gr

[gmx-users] problem with energy minimization

dear gromacs user i am doing simulation of Gal1p protein with ligand and without ligand.i made the system without ligand by removing the ligand from pdb file then i use pdb2gmx for generating topology file and editconf for adding box dimention and add spc water molecules.i have not face any problem

[gmx-users] problem with energy minimization

Dear gromacs user, I am doing simulation of Gal1P protein in explicit solvent.when i did energy minimization of system i got this warning:- Warning: 1-4 interaction between 2779 and 2788 at distance 1.005 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulat