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 <tec3.utah.edu>
To: amber.scripps.edu
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 15.0Å, 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 33Å to get the solute entirely inside the box.
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Received on Fri Apr 18 2008 - 21:16:13 PDT
