[gmx-users] protein topology file fetal error

2013-01-26 Thread az kalsom
hi all, i am new to gromacs, when i run my protein file by following the tutorial example mention here( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html) I AM GETTING THE FOLLOWING ERROR FOR MY PROTEIN PDB FILE.. * Fatal error: Atom HA in residue SE

Re: [gmx-users] dna-drug simulations

2013-01-26 Thread Justin Lemkul
On 1/26/13 4:18 AM, amna khan wrote: hi, all , i want to simulate dna with ligand/drug i am getting error in generating he topology for dna . We can't help you unless you show us what the error is and provide (at the very least) your exact pdb2gmx command. I'm unable to do using the pd

Re: [gmx-users] protein-SWCNT md simulation

2013-01-26 Thread Justin Lemkul
On 1/26/13 4:23 AM, Atila Petrosian wrote: Dear all I want to simulate protein-SWCNT by gromacs. IFf there is a complete tutorial about that, please introduce me. According to the Andrea Minoia's tutorial, there is no problem for MD simulation of the CNT solitude. I have many question about si

Re: [gmx-users] protein topology file fetal error

2013-01-26 Thread Justin Lemkul
On 1/26/13 4:41 AM, az kalsom wrote: hi all, i am new to gromacs, when i run my protein file by following the tutorial example mention here( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html) I AM GETTING THE FOLLOWING ERROR FOR MY PROTEIN PDB FI

[gmx-users] make_ndx error

2013-01-26 Thread Albert
Hello: I am using make_ndx to make a index file in Gromacs 4.6, make_ndx -f input.pdb but it said: Copied index group 1 'Protein' Copied index group 25 'Water_and_ions' One of your groups is not ascending Group is empty thank you very much best Albert -- gmx-users mailing listgmx-users

Re: [gmx-users] make_ndx error

2013-01-26 Thread Justin Lemkul
On 1/26/13 12:25 PM, Albert wrote: Hello: I am using make_ndx to make a index file in Gromacs 4.6, make_ndx -f input.pdb but it said: Copied index group 1 'Protein' Copied index group 25 'Water_and_ions' One of your groups is not ascending Group is empty What exactly did you enter a

Re: [gmx-users] make_ndx error

2013-01-26 Thread Albert
On 01/26/2013 06:53 PM, Justin Lemkul wrote: What exactly did you enter at the make_ndx prompt? -Justin 1|25 protein, water and ions -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs

[gmx-users] probems using drude oscillator with ions SWM4-NDP model

2013-01-26 Thread 姚懿
Dear gmx users, When I using the drude oscillator model in gromacs, using the SWM4-NDP forcefield with ions in it. I have this kind of problem. Which will cause the calculation failed. Can you give me some advice. = step 11868: EM d

Re: [gmx-users] make_ndx error

2013-01-26 Thread Justin Lemkul
On 1/26/13 1:30 PM, Albert wrote: On 01/26/2013 06:53 PM, Justin Lemkul wrote: What exactly did you enter at the make_ndx prompt? -Justin 1|25 protein, water and ions What types of ions do you have? I can reproduce this problem for a protein with ions bound to it, which are numb

Re: [gmx-users] make_ndx error

2013-01-26 Thread Albert
On 01/26/2013 07:41 PM, Justin Lemkul wrote: What types of ions do you have? I can reproduce this problem for a protein with ions bound to it, which are numbered discontinuously with water and ions in solution. -Justin thank you for kind reply. I only have Na+ and Cl-. best Albert -- gm

Re: [gmx-users] make_ndx error

2013-01-26 Thread Justin Lemkul
On 1/26/13 1:49 PM, Albert wrote: On 01/26/2013 07:41 PM, Justin Lemkul wrote: What types of ions do you have? I can reproduce this problem for a protein with ions bound to it, which are numbered discontinuously with water and ions in solution. -Justin thank you for kind reply. I only ha

Re: [gmx-users] make_ndx error

2013-01-26 Thread Albert
On 01/26/2013 07:51 PM, Justin Lemkul wrote: Can you please post the following: 1. The groups printed in the make_ndx prompt 2. The output of gmxcheck on an index file created from your coordinate file (created simply by typing 'q' at the prompt, i.e. not creating any special groups) -Justi

Re: [gmx-users] make_ndx error

2013-01-26 Thread Justin Lemkul
On 1/26/13 1:57 PM, Albert wrote: On 01/26/2013 07:51 PM, Justin Lemkul wrote: Can you please post the following: 1. The groups printed in the make_ndx prompt 2. The output of gmxcheck on an index file created from your coordinate file (created simply by typing 'q' at the prompt, i.e. not cr

Re: [gmx-users] error about pbc

2013-01-26 Thread Kieu Thu Nguyen
Thank Tsjerk so much ! But after being minimized 5 steps and equilibrated 90 ns, there are some bonds in the system that rotate more than 30 degrees. I applied tips for blew up system as you advised. But the system does not achieve balance. Should i carry out more many steps for minimization ?

Re: [gmx-users] error about pbc

2013-01-26 Thread Justin Lemkul
On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote: Thank Tsjerk so much ! But after being minimized 5 steps and equilibrated 90 ns, there are some bonds in the system that rotate more than 30 degrees. I applied tips for blew up system as you advised. But the system does not achieve balance. Should