AMBER Archive (2008)

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

From: Waqas Nasir (nasirwaqas1983_at_yahoo.com)
Date: Thu Sep 04 2008 - 05:15:37 CDT

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.

      
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