Re: [gmx-users] sphere around a protein

Hi Justin, Revisiting some of the calculations I had tried to do few days back. Just as a recap I am trying to build a sphere around the protein. As you had suggested in the last messgae of this thread to make a new directory. I did that. I used the following commands: editconf -f 1li.gro

Re: [gmx-users] sphere around a protein

shivangi nangia wrote: Hi Justin, Revisiting some of the calculations I had tried to do few days back. Just as a recap I am trying to build a sphere around the protein. As you had suggested in the last messgae of this thread to make a new directory. I did that. I used the following

Re: [gmx-users] sphere around a protein

Hi Justin, Thanks a lot! Things worked. Now I, however, have a different problem in extension to what I am doing. I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion. editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro

Re: [gmx-users] sphere around a protein

shivangi nangia wrote: Hi Justin, Thanks a lot! Things worked. Now I, however, have a different problem in extension to what I am doing. I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion. editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox

Re: [gmx-users] sphere around a protein

Justin A. Lemkul wrote: shivangi nangia wrote: Hi Justin, Thanks a lot! Things worked. Now I, however, have a different problem in extension to what I am doing. I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion. editconf -f 1li.gro -c -box 12 12

Re: [gmx-users] sphere around a protein

Hi, Please correct me if I am wrong. In that case then, I will have polyhisitine in the box size 12 12 12 and then If I add dhb anions and Li cations, they will be placed randomly in the box. When I add then the 1 Li cation, water methanol sphere, how is it necessary it will cover/solvate all

Re: [gmx-users] sphere around a protein

shivangi nangia wrote: Hi, Please correct me if I am wrong. In that case then, I will have polyhisitine in the box size 12 12 12 and then If I add dhb anions and Li cations, they will be placed randomly in the box. When I add then the 1 Li cation, water methanol sphere, how is it

Re: [gmx-users] sphere around a protein

shivangi nangia wrote: Hi Justin, I used 15 nm cubic box and 6 nm shell. I again tried to insert only 1 histidine molecule in the sphere. I get the same error Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become

[gmx-users] sphere around a protein

Hi Justin and other gmx-users, I want to make a sphere around a protein (5nm).with Li ions and anions. Justin, as you had suggested to use genbox -shell option, I tried using it but i realized that since my protein is a long tube like structure, the shell option generated a cyclinder around the

Re: [gmx-users] sphere around a protein

shivangi nangia wrote: Hi Justin and other gmx-users, I want to make a sphere around a protein (5nm).with Li ions and anions. Justin, as you had suggested to use genbox -shell option, I tried using it but i realized that since my protein is a long tube like structure, the shell option

Re: [gmx-users] sphere around a protein

Hello, Thanks Justin, I am getting somewhere but still running into problems. Okay, I have a 6 nm sphere (one Li ion surrounded by 1:1 water-methanol mixture) in 12 nm box. I did the following: editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro

Re: [gmx-users] sphere around a protein

shivangi nangia wrote: Hello, Thanks Justin, I am getting somewhere but still running into problems. Okay, I have a 6 nm sphere (one Li ion surrounded by 1:1 water-methanol mixture) in 12 nm box. I did the following: editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox -cp

Re: [gmx-users] sphere around a protein

Dear Justin, No. I am still preparing the system. I want the protein in the solvent sphere. On Sun, May 8, 2011 at 9:29 PM, Justin A. Lemkul jalem...@vt.edu wrote: shivangi nangia wrote: Hello, Thanks Justin, I am getting somewhere but still running into problems. Okay, I have a

Re: [gmx-users] sphere around a protein

shivangi nangia wrote: Dear Justin, No. I am still preparing the system. I want the protein in the solvent sphere. I see now. You're setting a 12-nm cubic box, but then using a shell of 6 nm, which causes neighbor searching to occur throughout the entire box. The maximum value of

Re: [gmx-users] sphere around a protein

Hi Justin, I used 15 nm cubic box and 6 nm shell. I again tried to insert only 1 histidine molecule in the sphere. I get the same error Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. On