Re: [gmx-users] Protein in GdmCl solution

2013-02-18 Thread Biswajit Gorai
n the temperature effect nullifies. Showing GdmCl producing counteraction to temperature, which experimentally doesn't valid for my target. Looking forward for your reply. Thanking you. Biswajit On Mon, Feb 18, 2013 at 6:55 PM, Justin Lemkul wrote: > > > On 2/18/13 6:29 AM, Biswajit Gor

Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

2012-03-27 Thread Biswajit Gorai
Dear Bipin, Edit your topology file as: ### ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Ion_chain_A2.itp" *#include "oct.itp"* ; Include water

Re: [gmx-users] Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q

2012-03-20 Thread Biswajit Gorai
Dear Lemkul, Thanks. Can any one suggest how/where to get the correct .itp file for Guanidinium Chloride? Regards Biswajit On Tue, Mar 20, 2012 at 5:32 PM, Justin A. Lemkul wrote: > > > Biswajit Gorai wrote: > >> Dear GROMACS users, >> >> I am beginner to

[gmx-users] Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q

2012-03-20 Thread Biswajit Gorai
Dear GROMACS users, I am beginner to GROMACS. I want to simulate my protein in different concentrations of Guanidinium Chloride solution and collected the files (3M & 5M box and .itp file) from http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies. Then I build a topology file 't