Re: [AMBER] question about bond command

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Thu, 22 Jul 2010 14:55:48 -0700

> Why should I use bond command for my constructed by hand pdb file?

No need to if all your residues connect as strands, i.e. each
is bonded to no more than 2 other residues. Read my first reply
again. (If leap parsed CONECT records in pdb, this would be an
alternative to using bond.)

> My other concern, when i try the desc command on my 4 defined
> residues all have tail and head. Is this normal?

For residues that form the body of a strand, yes.

> The thing is all my residues "RESD" are terminal
> groups, so I guess they need to have just head.

I.e. the head residue itself is not one of the ones you defined,
and all your residues are tails attached to other residues.

> If this is correct how to eliminate tail in "RESD".

Probably no need, though you will want a TER in pdb after
each of your residues so that it won't be bonded to the next.


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Received on Thu Jul 22 2010 - 15:00:04 PDT
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