Hello Yoanes--
> My name is Yoanes Maria Vianney from UGhent. I want to calculate a 30-nt
> DNA-testosterone complex structure. For that I have prepared the basic files
> (PDB, psf, par, restraints, etc) and start to calculate by DGSA using the
> start_structures.py script.
> However, in the beginning of the calculation, there is a message in the log
> file showing
>
> AT_Build::buildNode: cycle link found between atoms 31 LIG C4 and
>
> 31 LIG C3
> removing bond.
> AT_Build::buildNode: cycle link found between atoms 31 LIG C9 and
>
> 31 LIG C10
> removing bond.
> AT_Build::buildNode: cycle link found between atoms 31 LIG C14 and
>
> 31 LIG C8
> removing bond.
> AT_Build::buildNode: cycle link found between atoms 31 LIG C17 and
>
> 31 LIG C13
> removing bond.
>
This message by itself may not indicate a problem, but the message
should disabled when you add the lines
dyn.breakAllBondsIn("resname LIG")
or
dyn.group("resname LIG")
where dyn is each IVM object.
> As such, the testosterone is not in a proper aliphatic ring anymore.
Are you saying that the covalent geometry of the ligand is incorrect?
This would indicate that the associated PSF is incomplete - missing
bonds, angles or impropers. How was this PSF created? If you wish to
treat the ligand as a rigid body, then the group option above must be
chosen, and resname LIG must be excluded in the selection when calling
fixupCovalentGeom.
I hope my response is on the right track.
best regards--
Charles
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