AMBER Archive (2003)

Subject: Re: AMBER: combine prep files

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 29 2003 - 19:27:57 CDT

On Wed, Jul 30, 2003, Mi-Kyung Seo wrote:
>
> I am trying to perform MD for carbohydrates with AMBER 7.0
> I want to combine and make polysacchrides with Woods each carbohydrate prep
> fragment. (from Glycam web)
>
> I tried "combine" and "bond" command in XLEaP but I can't open combined
> prep and structure is not correct.

Although details are sketchy (just saying "structure is not correct" is not
very helpful), combine, followed by bond should work; but you don't want to
save the result to a prep file: only individual residues should go in prep
files. Generally, once you have used combine or sequence to make a polymer,
you would use saveAmberParm to store it.

>
> When I build new molecule and save it using "saveamberprep" in XLEaP, prep
> file format is different from Woods prep format.

There are indeed different kinds of prep file, but I would not recommend
saving in any of them. [Although the saveAmberPrep command is still in the
code, it is not even in the Users' Manual, because we are trying wean users
away from it, while still not breaking existing scripts.] I would recommend
the saveOff command instead for anything you create.

If you need to do it, antechamber has the capability of converting Cartesian
prep (prepc) files into internal coordinates (prepi). I haven't tried this
conversion myself, but it is supposed to work.

...good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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