CORAL Domain grouping is not compatible with initial

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
Post Reply
Message
Author
mawhite
Active member
Posts: 21
Joined: 2011.08.15 22:18
Location: UTMB, Galveston, TX

CORAL Domain grouping is not compatible with initial

#1 Post by mawhite » 2018.01.25 20:18

Hello,

CORAL is still giving errors when grouping certain domains. The simplest is a two domain heterodimer interacting through each CT domain

ANT-ACT:BCt-BNt

Code: Select all

DImer.con
ANT
LINK 4
ACT
CTER 6
BNt
LINK 4
BCt
CTER 6

Code: Select all

coral << ...
Dimer.con
No
No
No
No
2,4
0,0
####
produces the infamous "Domain 2: grouping is not compatible with initial configuration" error.

To fix this problem I reverse all the chains, co that the CT are the first PDB in DimerReversed.con

Code: Select all

tac ANT > TNA; tac ACT > TCA; tac BCt > tCB; tac BNt > tNB

Now grouping the two CTermial domains as 0,1 works.

Code: Select all

DImerReversed.con
NTER 6
TCA
LINK 4
TNA
NTER 6
tCB
LINK 4
tNB

Code: Select all

coral << ...
DimerReversed.con
No
No
No
No
1,3
0,0
....
  ====  Simulated annealing procedure started  ====
####

The result is the inverted D-amino acid structure, which produces identical results to the normal L-amino acid structure, but is not physical, and is an accounting nightmare if using any inter residue restraints.

This is a terrible work-around. Why will CORAL not allow the second domain to be grouped (or fixed)?

Best regards,
Mark

Post Reply