Re: [gmx-users] DNA simulations

2012-07-01 Thread Mark Abraham
On 1/07/2012 7:31 AM, SatyaK wrote: Hello All, I am working on DNA simulations using GROMACS Question: I created A.gro file that has DNA molecule and water molecules within a box using GROMACS. I want to create a cylinder around the DNA so that I can place some ions, or, compute axis of DNA

Re: [gmx-users] atom type

2012-07-01 Thread Mark Abraham
On 1/07/2012 1:16 AM, Shima Arasteh wrote: Hi dear gmx friends, I have a C atom which its neighbors are N, O, H atoms and then sp2 hybridization. I wanna add this atom to the CHARMM36, but I don't know its atom type. Neither can we. Your description could be of H-C(=O)-NXY or H-C(=NX)-OY.

Re: [gmx-users] Structure optimization failure

2012-07-01 Thread Mark Abraham
On 30/06/2012 10:18 PM, ms wrote: On 29/06/12 19:59, Justin A. Lemkul wrote: Wouldn't it be nice to create a table of "standard settings" for each forcefield in the gmx documentation (with lit references of course)? Well, anyone is welcome to submit anything they feel would be useful... ;)

Re: [gmx-users] chi1/chi2

2012-07-01 Thread Mark Abraham
On 28/06/2012 8:07 PM, Raj wrote: during the simulation. I tried g_chi to obtain chi1 and chi2 values at the end I'm getting the plot withe values ranges from -180 to 180 . But in papers people have reported in 360 degree how can i get the data. Please give me suggestions The data is periodic

Re: [gmx-users] Re: COM Pulling

2012-07-01 Thread Justin A. Lemkul
On 7/1/12 12:02 AM, Raj wrote: Dear Justin, I've tried what you have suggested. I have used the pull code and gave 4 amino acid residues as a reference group. The location of the groups are one below the ligand (in the protein core) and 3 were on the above ( towards the active site gorge). Whe

[gmx-users] Computing vectors normal (perpendicular) to molecules

2012-07-01 Thread Andrew DeYoung
Hi, Suppose that I have a system of benzene molecules (in reality, my system is more complicated, but for my question, it will be simpler to consider just an ensemble of benzene molecules). I would like to find a vector normal (i.e., perpendicular) to the plane of each benzene molecule in my sy

Re: [gmx-users] Computing vectors normal (perpendicular) to molecules

2012-07-01 Thread Mark Abraham
On 2/07/2012 6:50 AM, Andrew DeYoung wrote: Hi, Suppose that I have a system of benzene molecules (in reality, my system is more complicated, but for my question, it will be simpler to consider just an ensemble of benzene molecules). I would like to find a vector normal (i.e., perpendicular) to

Re: [gmx-users] Computing vectors normal (perpendicular) to molecules

2012-07-01 Thread Mark Abraham
On 2/07/2012 11:51 AM, Mark Abraham wrote: On 2/07/2012 6:50 AM, Andrew DeYoung wrote: Hi, Suppose that I have a system of benzene molecules (in reality, my system is more complicated, but for my question, it will be simpler to consider just an ensemble of benzene molecules). I would like t

[gmx-users] Re: chi1/chi2

2012-07-01 Thread Raj
Dear Mark, Thanks for your reply.. can you suggest me how i can take the plot with 0 to 360 angle. I've tried periodic of g_chi with -all option to generate the chi1/chi2 plot for the each and every amino acid residue but i couldnt do it properly can you suggest on this. Thanks in advance -- View

Re: [gmx-users] Re: chi1/chi2

2012-07-01 Thread Mark Abraham
On 2/07/2012 12:20 PM, Raj wrote: Dear Mark, Thanks for your reply.. can you suggest me how i can take the plot with 0 to 360 angle. I've tried periodic of g_chi with -all option to generate the chi1/chi2 plot for the each and every amino acid residue but i couldnt do it properly can you suggest