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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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