Dear Amber Users,
I have followed amber tutorial A Room Temperature Ionic Liquid to create the initial structure. I have succesfully generated the mol2 file which corresponds to the acetonitrile but for the bmim i couldn't be able to generate the mol2 file successfully. One thing which is not clear to me is that during building of structure of bmim in xleap should i draw double bond in imidazole ring and for BF4 do i need to correct the frcmod file manually as per the reference given in the tutorial. The frcmod for BF4 and mol2 file for bmim which i have got i have attached and these are different from the given corresponding files of tutorial. Also i would like to mention that the z coordinates in the pdb generated are 0 for all the three cases. Thanks in advance.
Shilpa Gupta
Research Scholar
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Received on Fri Sep 08 2017 - 22:00:03 PDT
