Hi,
I just started using AmberTools 1.4 and I am now able to successfully achieve some tutorials present on
http://ambermd.org/tutorials/. I try to repeat an exercise very similar to the B4 tutorial, but have some difficulties to complete the process. First, I am not able to run mopac with antechamber. I almost tried adding mopac.sh, but it is not functional. So I tried to run antechamber with sqm to get the charges, but I get a "segmentation Fault". My main concern is about the number of atoms of my organic molecule. The compound is a Trimer with a total of 230 atoms. Is there a limit in ambertools regarding the number of atoms? I also tried to calculate the charges using my own version of mopac, using mainly babel to convert my file in a mol2 file, but I still face a problem in the molecular dynamics. The movements seems erratic. Am I the first to face this situation? Thanks,
Marc-André Dubois
Université de Montréal
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Received on Thu Jan 20 2011 - 15:00:05 PST
