[gmx-users] Double entries in block structure--problem with SHAKE

Justin Lemkul jalemkul at vt.edu
Wed Nov 7 19:24:03 CET 2012

On 11/7/12 10:46 AM, tarak karmakar wrote:
> Dear All,
> As I am facing the following problem while using SHAKE to constrain
> some bonds, I have checked the mailing list but I think, this issue
> has not been resolved. So if anyone knows the solution kindly inform
> me.
> Program mdrun, VERSION 4.5.5
> Source code file: invblock.c, line: 79
> Fatal error:
> Double entries in block structure. Item 5247 is in blocks 1371 and 1370
>   Cannot make an unambiguous inverse block.
> Actually I need to fix some of the ligand bonds along with the
> covalent h-bonds (C-H, N-H, O-H etc.).
> What do you suggest to use for this multiple constraining problem ?
> Should I use SHAKE/LINCS for both type of bonds or anything else ?

Can you explain in a bit greater depth what you're trying to do?  Are you trying 
to constrain distances between atoms that are not covalently bonded?  In that 
case, restraints are likely more appropriate than constraints, but we'll need 
more detail before anyone can give you any really productive suggestions.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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