[AMBER] sleap log

From: Omair A. Khan <oak3.psu.edu>
Date: Tue, 1 Jun 2010 12:10:10 -0400

Hello everyone,

Since tleap isn't working with Fedora Core 12 x86_64 (and other Linux
flavors too, it seems), I've switched over to sleap as everyone has
suggested. I find that sleap is a lot cleaner and more computationally
efficient, but I have a few questions. This post is long but I've
tried to organize it so it's not difficult to read.

The leap.log has been removed from sleap. Since all information is
dumped to standard output now, I've been piping it to create my own
log files. I've found that a lot of information that was found in
leap.log is now missing. I will reference the tutorial for xleap at

> To add a truncated octahedral box of water around our DNA we use the solvateoct command. Since in
> the course of this demonstration we have already solvated our "model" with a rectangular box of water
> we shall use the copy we made "model2". Enter the following in xleap to create the water box (note: if
> you are using AMBER7 use WATBOX216 in place of TIP3 PBOX):
> solvateoct model2 TIP3PBOX 8.0
> This should give the following output:
> > solvateoct model2 TIP3PBOX 8.0
> Scaling up box by a factor of 1.320477 to meet diagonal cut criterion
> Solute vdw bounding box: 24.918 26.588 39.153
> Total bounding box for atom centers: 60.281 60.281 60.281
> (box expansion for 'iso' is 65.4%)
> Solvent unit box: 18.774 18.774 18.774
> Volume: 115065.025 A^3 (oct)
> Total mass 59917.340 amu, Density 0.865 g/cc
> Added 2968 residues.

My sleap log does not give the scaling factor, mass, density, etc.
when I call the solvateoct command. How can I get this information? My
script is located at http://pastebin.com/v3SJWMgX and my log is here:

I am also confused as to what lines 187-192 in the log mean. How does
this relate to the dimensions of the box? Further down I see box
dimensions, but I don't know how to interpret them. The "svt size"
must be the solvent unit box (since it's the same as that in Ross's
tutorial), but what are "rgn size" and "nx,ny,nz"? This is the first
time I'm using a truncated octahedral box so I apologize if this is
common sense.

And finally, does the setpchg command add ions or get rid of the
partial charges in the molecule? If it does add ions, how does it
differentiate between Na+ and K+, for example?

Thank you in advance,

Omair Khan

AMBER mailing list
Received on Tue Jun 01 2010 - 09:30:04 PDT
Custom Search