AMBER Archive (2008)

Subject: Re: AMBER: No bond and angle parameters for - -?????

From: Lachele Foley (Lists) (lf.list_at_gmail.com)
Date: Thu Sep 04 2008 - 09:03:08 CDT

Just out of curiosity.. Why did you add a hydrogen to the ZLB
residue? That might not give the results you had in mind, and might
have a lot to do with the error messages. Which hydrogen did you add?

On Thu, Sep 4, 2008 at 6:15 AM, Waqas Nasir <nasirwaqas1983_at_yahoo.com> wrote:
> Hi,
>
> I am getting following output while performing the check on the sugar unit
> just created.
>
>
>
> Checking for bond parameters.
> No bond parameter for: -
> No bond parameter for: -
> No bond parameter for: -
> No bond parameter for: -
> No bond parameter for: -
> No bond parameter for: -
> No bond parameter for: -
> No bond parameter for: -
> No bond parameter for: -
> No bond parameter for: -
> No bond parameter for: -
> .
> .
> [and the list goes on]
>
> Checking for angle parameters.
> Can't find angle parameter: - -
> Can't find angle parameter: - -
> Can't find angle parameter: - -
> Can't find angle parameter: - -
> Can't find angle parameter: - -
> Can't find angle parameter: - -
> Can't find angle parameter: - -
> Can't find angle parameter: - -
> Can't find angle parameter: - -
> Can't find angle parameter: - -
> Can't find angle parameter: - -
> Can't find angle parameter: - -
> .
> .
> [and the list goes on]
>
> There are missing parameters.
> check: Warnings: 14
> Unit is OK.
>
> Is it ok to work with it, because apparently there is nothing wrong with the
> unit every parameter is there and the net charge is also zero, its just that
> I added a hydrogen manually to one of the oxygens in ZLB residue. And
> moreover, the top and crd files are also generated smoothly without any
> warning and same is the case for lib file.
>
> Any thoughts...
> Thanks,
> Regards,
> Waqas.
>
> PS: I am using amber version 8 with glycam06 force field downloaded from
> glycam website.
>
> 

-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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