Dear gmx-users, I tried to minimize my systems formed by a protein obtained by homology modelling procedure, in one case with a ligand inside, in the other case in the apo form. All worked fine until the minimization step: when I launched mdrun, the well known "stepsize too small..." communication appears. The program worked for 37 steps without producing output energies, and the final report was: Potential Energy = -6.07e+5 (for the prot+lig); -5.58e+5 (for the protein alone) Maximum force = inf on atom 1 Norm of force = inf I had a look to the gmx-user list archive, but when the "stepsize too small" error is reported, generally the potential energy is very high. In my case, the potential energy seems to be correct (it is negative, and the order of magnitude is similar to that of other systems I studied before). Usually when I retrieve this error, either the potential energy is very positive and high, or there are errors in the protein, but I visualized the systems with VMD and they seem to be correct. It would sound VERY strange if I had the protein already in a minimum of potential energy!!! Moreover, the same thing happens in both cases, so I don't think it's a problem related to the ligand. What do you think about? Could you give me some hint? Thank you very much and best regards Anna __________________________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm "If you think you're too small to make a change, try sleeping with a mosquito"
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