Re: [AMBER] Problems using library file containing multiple residues to make a complex

From: Daniel Roe <>
Date: Tue, 6 Jul 2010 08:54:28 -0400

On Tue, Jul 6, 2010 at 5:05 AM, Chris Whittleston <> wrote:
> Sorry to be unclear - I do load those parameters, I just did not show the
> very top of the tleap output to save space.
> The top is indeed 'source leaprc.ff99SB'

Sorry, going back through your email I see it was in the middle, I
missed it in all the text.

I think the issue may be in creating your library file, when you try
to use one mol2 file to save several residues. When you're creating
the library file you're only creating something called LIG, as
evidenced when you load it back into leap:

> loadoff Siaa_6Galb_4GlNb.lib
Loading library: ./Siaa_6Galb_4GlNb.lib
Loading: LIG

I think the saveoff command can only be used to create 1 residue at a
time. So your OME, NAG, etc end up inside LIG. I think what you would
have to do is split up your mol2 file into the separate residues and
save each library separately, e.g.:

OME=loadmol2 Siaa_6Galb_4GlNb-OME.mol2
check OME
saveoff LIG Siaa_6Galb_4GlNb-OME.lib

Repeat for the rest.

Just out of curiosity, why not use GLYCAM parameters for your sugar component?


Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ   08854
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Received on Tue Jul 06 2010 - 06:00:04 PDT
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