AMBER Archive (2003)

Subject: AMBER: saveamberprep in xLeap

From: Mi-Kyung Seo (mkseo98_at_hotmail.com)
Date: Thu Aug 07 2003 - 22:38:24 CDT

Hello amber users,

I build disacchride (two galactose) in xLeap and Unit contains two residues
when I use "desc" command.
I save it in prep format using saveamberprep command but it says the
following message.

>saveamberprep unit myunit.prep

  saving prep, residue UNK
  UNK: connect0 not defined
  UNK: connect1 not defined
  saving prep, residue UNK
  UNK: connect0 not defined
  UNK: connect1 not defined
  -- Remember to delete unwanted IMPROPER terms!

I tried to use "set unit.1 connet0 unit.1.XX" and "set unit.1 connect1
unit.1.YY"
Which atoms do I need to use for XX/YY? any atoms in residue 1??
Do I need to use the above same command for residue2?

Thanks in advance.
Mikyung

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