AMBER Archive (2009)

Subject: Re: [AMBER] Residues

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Jun 18 2009 - 16:13:53 CDT

> I had used the following
> set q1 tail q1.1.atom name
> I had made the connections by defining a new tail each time and make the
> connectivity .In my pdb file obtained after minimization from the topology
> and coordinate files has TER cards separating each of fragment .

Since pdb is a linear format (one residue follows another), it will
be impossible to have 3 residues immediately following an initial one.

Assuming r1 is bonded to r2,r3,r4:

E.g. if your residue order in the pdb is r1, r2, r3, r4, r1-r2 are
bonded so no TER between them. But r3 is not bonded to r2, so there
needs to be a TER between them. And so on.

Bill

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