TinkerTools/tinker

How do I create disulfide bonds with `protein`?

CanisW opened this issue · 0 comments

Recently I have been trying to build tinker xyz files for peptides that has disulfide bonds with the protein program in tinker. There is only a very simple instruction for how to build disulfide bonds, but I cannot figure out what the correct format to input the disulfide partner is.

 Enter One Residue Name per Line as the Standard Three-Letter Code, and
 optionally, Phi-Psi-Omega Angles (3F), Chi Angles (4F), Disulfide Partner
 if CYX Residue (I), and D/L Chirality (A1)

I have tried several ways (e.g. the one below), but it kept giving me errors.

 Enter Residue   1 :  CYX 2

 Enter Residue   2 :  MOL

 Enter Residue   2 :  CYX 1

 Enter Residue   3 :

 Cyclize the Polypeptide Chain [N] :
At line 953 of file protein.f
Fortran runtime error: Index '0' of dimension 1 of array 'disulf' below lower bound of 1

Error termination. Backtrace:
#0  0x7f4f597cc1aa
#1  0x7f4f597ccd19
#2  0x7f4f597cd0fb
#3  0x406bde
#4  0x414ad0
#5  0x41984d
#6  0x419f41
#7  0x7f4f58e48492
#8  0x4015bd
#9  0xffffffffffffffff

Thank you!