AMBER Archive (2003)

Subject: Re: AMBER: variable not in namelist for Sander input

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Mon Jul 21 2003 - 11:40:29 CDT

I tested the input in both AMBER6 and AMBER7...

> ntwxm=0,
> ntwem=0,

With AMBER6, remove the two variables above. With AMBER7 ndfmin is no
longer specified in the input. With these changes, the input file seemed
to run OK with my system.

Note that my debugging effort was simplified since some compilers /
namelist implementations are a little more friendly on failure and specify
what variable was not recognized. I tested on a SGI...

> times and I can not find where the errors are. By the way, can anyone give
> me some references on using PME for an octahedral system for
> metalloprotein (like zinc-containing protein)?

I do not have any references handy, but note that Zinc can be difficult
since the pairwise additive force field may not be sufficient to fully
represent its properties. Despite this, a number of MD publications have
used Zn and if you are mostly concerned with the structure, things may be
OK. A pubmed search (+molecular +dynamics +zinc) pulled up lot's of
references...

Good luck,

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
| Departments of Medicinal Chemistry and of University of Utah
| Pharmaceutics and Pharmaceutical Chemistry 30 South 2000 East, Room 201
| & Center for High Performance Computing Salt Lake City, Utah 84112
|
| e-mail: tec3_at_utah.edu phone: (801) 587-9652 FAX: (801) 585-9119
\ http://www.chpc.utah.edu/~cheatham Offices: BPRP295A / INSCC 418

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