Re: AMBER: how to combine two molecules

From: Benjamin Juhl <itbbju.itb.uni-stuttgart.de>
Date: Fri, 10 Aug 2007 11:11:07 +0200

Hi,

it might be that there are problems with the atom types. AFAIK, O3 and
C3 are not normal atom types the forcefields (rather OS and CT), so the
parameters for these bonds and angles are missing.
If you supplied the mol2 file, perhaps someone could have a look at it.

Benjamin

Wenyong Tong schrieb:
>
> Hello Amber Users,
>
>
>
> I have two pdb files: one is sugar produced by Leap; another is lipid,
> and I used antechamber to get .prepin and frocmod files.
>
>
>
> I wonder how to combine these two molecules. I tried the Leap:
> "Sequence" command and it seems the distance is a problem. I tried
> using Insight II to combine them and .mol2 files. When I loaded this
> file into Leap and check unit, I got the following message:
>
>
>
> Checking for bond parameters.
>
> Could not find bond parameter for: O.3 - C.3
>
> Could not find bond parameter for: O.3 - C.3
>
> .
>
>
>
> Checking for angle parameters.
>
> Could not find angle parameter: O.3 - C.3 - O.3
>
> .
>
>
>
> I compared the Prepin and glycam04.prep files with my .mol2 files.
> There are no differences of atom name among those files.
>
>
>
> Anyone can give me some suggestions? Thanks in advance!
>
>
>
> Wenyong
>
>
>
>
>
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Received on Sun Aug 12 2007 - 06:07:47 PDT
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