Bond Length Constraints

[Arnold Paecklar]

Hello Bashir,

I hope you are doing well these days!

I was trying to use bond length constraints, but it does not seem to be working. I checked the structure with VESTA and the length distributions with the program Diamond. For example, I set 2-2.85 A for certain Bi-O bonds, but the output structure has bond lengths that extend down to 1.6 A which corresponds to what was set for the IntraMolecularDistanceConstraint. The smallest Bi-O bond in the starting structure is 2.1 A. I probably just overlook something, but could you tell me whether I made some mistake with how I defined these bond length constraints for this modelling system or whether there is some other issue with how the bond lengths need to be defined?

I will send the files to your email address.

Thank you in advance for your time!

With best wishes and kind regards,
Arnold

[Bachir Aoun]

Hey Arnold,

i can think of two things that might have happened.

• definitions are case sensitive, so 'Bi-O' is not the same as 'bi-O' or 'bI-O' for instance. so you might have set something wrong there
• when you initial structure has bad distances, the engine tries to minimize the total error for the constraint and sometime this will introduce new wrong distances. to avoid that you should set the flag flexible to False

hope that helps