AMBER Archive (2009)

Subject: Re: [AMBER] Residues

From: Roman Osman (roman.osman_at_mssm.edu)
Date: Thu Jun 18 2009 - 16:58:53 CDT

But you can insert TER where you want an interruption in sequence and
then build an explicit bond between the respective residues.
My student did that the following way:
e.g.,
r1
r2
TER
r3
r4
TER
r5
then bond r2 r4
and bond r3 r5
of course the usual care of choosing the right atoms needs to adhered
to.
Rami

On Jun 18, 2009, at 5:13 PM, Bill Ross wrote:

>> 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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Roman Osman
roman.osman_at_mssm.edu

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