AMBER Archive (2004)

Subject: Re: AMBER: xleap don't recognize formaldehyde?

From: David A. Case (case_at_scripps.edu)
Date: Tue Apr 27 2004 - 13:56:30 CDT

On Tue, Apr 27, 2004, scopio wrote:
>
> I have a pdb contains a residue called 'FOR'. It consists of only two
> atoms which are C atom and O atom. I think 'FOR' stand for formaldehyde.
> My problem is that Xleap don't recognize this residue.

You need to create a formaldehyde residue. The simplest way to do this
is to use the antechamber suite, although formaldehyde is so simple you
could almost do it "by hand" using xleap. (The "biotin/strepavidin" tutorial
has a example of building a new residue inside leap.)

...good luck...dac 

-- 

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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
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