leena
Dear all,
I have tried to use RBD, BDB() and RTA macros in the Simulated Annealing procedure. Unfortunately, TOPAS gave an error as follows:
Error loading sstring_in at
{BDB}
unknown or misplaced keyword.
Here is the syntax I used:
rigid
z_matrix C1
z_matrix C2 C1 RBD 1.401 BDB(1.401)
z_matrix C3 C2 RBD 1.399 BDB(1.399) C1 118.384
z_matrix C4 C3 RBD 1.397 BDB(1.397) C2 120.289 C1 0.0
z_matrix C5 C4 RBD 1.401 BDB(1.401) C3 119.781 C2 360.0
z_matrix N C1 RBD 1.364 BDB(1.364) C5 29.123 C4 180.0
z_matrix C6 C5 RBD 1.489 BDB(1.489) N 121.105 C1 180.0
z_matrix C7 C2 RBD 1.479 BDB(1.479) C3 120.744 C1 180.0
z_matrix O1 C7 RBD 1.272 BDB(1.272) C2 120.472 C3 180.0
z_matrix O2 C7 RBD 1.272 BDB(1.272) O1 119.057 C2 RTA 180.1
...
I would appreciate any hint or suggestion.
rowlesmr
Maybe a stupid question, but where have you defined the RBD, BDB() and RTA macros? I can't find them in my Topas installation.
leena
I have found them in the Topas 5 Tutorial file, page 116: "3.2.2 Creation of a rigid body for Cimetidine using a z-matrix representation" chapter. The chapter explains how to refine distances and torsion angles of a rigid body using macros RBD,BDB for the distances and RTA,TAB for the angles.
In my input file I have a rigid body represented by its z-matrix. I would like to add additional degrees of freedom - torsion angles that the rigid body has. When I start simulated annealing the program gives an error, so it seems that BDB and RTA macros cannot be used in an input file.
rowlesmr
Ah, I see now.
You need to define those macros yourself.
You need to put the following definitions in your input file
macro RTA { @ }
macro TAB(v1, v2)
{
min = v1; max = v2;
}
macro RBD { @ }
macro BDB(v)
{
min = v - .1; max = v + .1;
}
When you've done that, you can use them freely.
You can alter the definition of RBD from { @ } to { } in order to turn off the refinement, or change the 0.1 in BDB to change the bond length bounds.
leena
Thank you very much. Indeed if I add the definitions of the macros, TOPAS starts the procedure. But I still have one question. My structure is represented by the rigid body + isolated atoms. When I start simulated annealing, I see that the rigid body is moving all over the unit cell, but tends to stuck in certain parts of the unit cell with complete overlapping of the atoms and with no physical meaning at all. The tech reference suggests to use anti-bump macros for the heavy atoms but what is the proper solution for light ones?