AMBER Archive (2000)

Subject: Re: leap problems

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Nov 07 2000 - 01:27:32 CST

        I am trying to build an imidazole ring using xleap.
        I am using the Draw option to get a five-membered
        ring. Unfortunately when I save using Build the
        ring opens to a chain. How can I avoid this ?
        I am using the Draw option to get a five-membered
        ring. Unfortunately when I save using Build the
        ring opens to a chain. How can I avoid this ?

Try not using Build - it only adds hydrogens & does what
it thinks is best for the geometry based on bond orders.
To save to a file,

> saveoff mymol mymol.off

Breaking a bond sounds like a bug, which I could investigate
if you saveoff a copy at the point before you do a Build.

        I am also trying to import a pdb file using leap.
        The program is not drawing any bond which causes
        problems when I save the topology file.

This is because the residue names do not appear in the library.
When there are templates for the residues in the library, leap

Alternatively, the pdb standard allows CONECT records to specify
bonds, and leap tries to make use of these if they are present.
In this case, you can see the bonds but still need to have residue
templates to saveamberparm. It is the missing atom information that
causes problems on saving the topolog file.

There is a tutorial on the amber web that covers making new residue
templates from pdb coordinates; or if the residue names in your file
just are different from the ones in the database (but the actual
residues are the same), you can use the addPdbResMap cmd to do the
mapping. Also see Deriving New Parameters on the amber web for
parameterizing new residues. In the end, I think the tutorials
will prove to be a time saver on the learning curve.

Bill Ross