Re: [gmx-users] Broken protein after EM

2012-08-27 Thread Justin Lemkul
On 8/27/12 8:27 AM, Shima Arasteh wrote: Dear gmx users, I'm simulating a protein in water. I ran these commands: 1.pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter 2.editconf -f monomer.gro -o monomer_newbox.gro -c -d 1.0 -bt cubic 3.genbox -cp monomer_newbox.gro -cs spc216.gro -o mono

[gmx-users] Broken protein after EM

2012-08-27 Thread Shima Arasteh
Dear gmx users, I'm simulating a protein in water. I ran these commands: 1.pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter 2.editconf -f monomer.gro -o monomer_newbox.gro -c -d 1.0 -bt cubic 3.genbox -cp monomer_newbox.gro -cs spc216.gro -o monomer_solv.gro -p topol.top 4.grompp -f ions.md

Re: [gmx-users] Broken protein chain.

2011-06-28 Thread Kavyashree M
Sir, Ok Thanks. With Regards M. Kavyashree On Tue, Jun 28, 2011 at 4:25 PM, Justin A. Lemkul wrote: > > > Kavyashree M wrote: > >> Dear users, >> >> Has anyone done simulation with a broken crystal structure? >> I know that it can be modeled before simulating. But I just wanted >> to know whet

Re: [gmx-users] Broken protein chain.

2011-06-28 Thread Justin A. Lemkul
Kavyashree M wrote: Dear users, Has anyone done simulation with a broken crystal structure? I know that it can be modeled before simulating. But I just wanted to know whether any one had done with the crystal structure having breakage as such without modelling. You need an intact starting s

[gmx-users] Broken protein chain.

2011-06-28 Thread Kavyashree M
Dear users, Has anyone done simulation with a broken crystal structure? I know that it can be modeled before simulating. But I just wanted to know whether any one had done with the crystal structure having breakage as such without modelling. Thanking you Respectfully M. Kavyashree -- gmx-users m

Re: [gmx-users] broken protein

2009-07-02 Thread Justin A. Lemkul
P.R.Anand Narayanan wrote: Dear users, How will I be able to run a simulation on a protein with 2chains if it is broken. I heard that the protein might have been broken which was observed from the failure of energy minimization which ended in just 1 step. "Broken" is a very generic term f

[gmx-users] broken protein

2009-07-02 Thread P.R.Anand Narayanan
Dear users, How will I be able to run a simulation on a protein with 2chains if it is broken. I heard that the protein might have been broken which was observed from the failure of energy minimization which ended in just 1 step. See the Web's breaking stories, chosen by people like you.