> 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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Received on Mon Jul 06 2009 - 10:04:14 PDT
