Re: [gmx-users] Problem with simulation of Protein-DNA complex

2012-02-20 Thread rarora
Hi Tsjerk, I have checked and re-checked the structure and it seems fine. I also made sure to minimise the starting structure really well after pdb2gmx. Although it did not achive required precision, but machine precision instead. Also, the problem starts with the NVT, before that everything

Re: [gmx-users] Problem with simulation of Protein-DNA complex

2012-02-09 Thread Tsjerk Wassenaar
Hi Rohit, Have you checked the atoms around 3460? It seems there's something wrong with your starting structure. Cheers, Tsjerk On Feb 9, 2012 2:09 PM, wrote: Hi Lina, I am sorry, I think I forgot to mention that I did perform energy minimisation using Steep-Descent for 5000 steps, before NV

Re: [gmx-users] Problem with simulation of Protein-DNA complex

2012-02-09 Thread rarora
Hi Lina, I am sorry, I think I forgot to mention that I did perform energy minimisation using Steep-Descent for 5000 steps, before NVT. I was so engrossed in other details that I forgot to mention it! Quoting lina : On Thu, Feb 9, 2012 at 8:44 PM, wrote: Dear Gromacs users, I have be

Re: [gmx-users] Problem with simulation of Protein-DNA complex

2012-02-09 Thread lina
On Thu, Feb 9, 2012 at 8:44 PM, wrote: > Dear Gromacs users, > > I have been trying to simulate a Protein-DNA complex using gromacs, but each > time I have been facing problems. I would like to point out that both the > Protein and DNA have been modeled and after that docked in order to obtain a

[gmx-users] Problem with simulation of Protein-DNA complex

2012-02-09 Thread rarora
Dear Gromacs users, I have been trying to simulate a Protein-DNA complex using gromacs, but each time I have been facing problems. I would like to point out that both the Protein and DNA have been modeled and after that docked in order to obtain a complex. Following are the parameters I am