AMBER Archive (2007)

Subject: Re: Fwd: RE: Re: AMBER: on PATH

From: M. L. Dodson (mldodson_at_houston.rr.com)
Date: Fri Jun 29 2007 - 08:34:08 CDT

Francesco Pietra wrote:
> Dear Ross:
> here again, just to say that I have learned that VMD is no substitute for
> xleap. However, my initial problems for amber9 will be dealt with through
> antechamber (no polymeric molecules, just very complex organic molecules of MW
> up to 3000 Da) and therefore may be leap/xleap are not directly called. I can
> provide pdb files (with hydrogens at right places) from a MM package, though I
> have to set explicit solvent, which is a problem for amber.
>
> As to why xleap resisted compilation, I remark that the X system - though
> perfectly functioning at 2D acceleration - lacks OpenGL, just because I was
> trying not to pollute too much with 32-bit libraries (or, that is my
> idiosyncrasy against 32 when the stuff is 64).
>
> I have to investigate whether OpenGL is now available pure 64-bit on debian. If
> so, probably my system can be adapted to the compilation of xleap.
>
> Thanks
>
> francesco
>

You almost never NEED to use xleap. There are only a few things that
you can do with xleap that you cannot do with tleap, the "terminal
interface" counterpart to xleap. xleap is required primarily for the
use of the "edit" and related commands when generating and modifying
structures. To prepare input files for the amber simulation programs,
you only need tleap. Setting solvent boxes for simulations is NOT a
problem for amber, just use tleap. Then you can look at the final
product in the molecular graphics program of choice, e.g., vmd.

I'll pass along what I have told students learning this program package:
put everything possible in shell scripts (which use antechamber, tleap,
etc). The scripts (plus the log files) exactly document everything you
did and make it easy to reproduce the sequence of steps the next time
you need to do something similar. You can even maintain them with a
revision control system.

Bud Dodson 

-- 
M. L. Dodson
Email:	mldodson-at-houston-dot-rr-dot-com
Phone:	eight_three_two-five_63-386_one
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu