AMBER Archive (2008)

Subject: Re: AMBER: Protein rotating out of box

From: Qiang Li (
Date: Wed Apr 02 2008 - 12:35:04 CDT

Hi, I meet the same problem too. I was following the tutorial on AMBER website, and I never manage to put the whole DNA into the box. I am using amber 8, Portland Group compiler, and AMD opteron. David A. Case just told me that the PGC should be the reason. Are you using PGC too? --Qiuting Hong ----- Original Message ---- From: Thomas Cheatham III <> To: Sent: Wednesday, April 2, 2008 9:54:46 AM Subject: Re: AMBER: Protein rotating out of box > Thanks for your comments. I guess the solvateoct is the way to go > here. However, after I solvate using the command: > 'solvateoct mol TIP3PBOX 15.0 0.78' parts of the solute is outside the > box. Hmm.. Does not the buffer argument, in this case 15.0┼, specify > the distance between the wall of the box and the closest atom? Or is > it the distance to the walls in the cubic box, and then it shawes off > the corners no matter if the solute is in the way? I have to make the > buffer as high as 33┼ to get the solute entirely inside the box. -------------------------- ____________________________________________________________________________________ You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost.
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