Hi Sir,
I have tried to reproduce a paper "PhysRevD.92.095021" for mSUGRA model. Basically, I am trying to reproduce the table-I of this paper. I have taken output for SPheno and micromega from SARAH-4.9.3.

Using the SPheno input file "LesHouches.in.MSSM", I am getting error like:
Warning from routine CalculateMSu
in the calculation of the masses
occurred a negative mass squared!

It is my humble request that you kindly clarify this issue.

Hi,

I'm not really surprised. These points are very fine-tuned: you have large soft masses and trilinear terms which at the end should end up in a light stop after a RGE running over 13 orders of magnitude. These calculations are very sensitive on all kind of different details and small changes can have a huge impact on the stop mass. SPheno uses a more advanced calculation of the Yukawa couplings than SUSY-HIT for instance. See for instance the recent paper 1703.03267 where the new method to obtain the running Yukawa couplings is explained.
Since the top Yukawa is the most important parameter in the running of the stop parameters, this makes most likely the difference. So, I guess you might need to adjust the values of A_0 and choose somehow smaller values to compensate for these effects.

Best,
Florian