The bond order in leap (changed by double-clicking on the bond) is only
useful for the xleap 'build' cmd, which applies simple hybridization
geometries. It sounds like you may be drawing a molecule in a planar
manner (z=0), and the 'build' cmd could fix that. Hardly anyone uses
these capabilities, preferring to import pdb files built with other
tools, but they are workable for small molecules/residues I think,
having debugged the original code in the 90's :-)
Bill
On 9/8/17 7:42 AM, guptashilpa_91.yahoo.com wrote:
> Dear Amber Users, \r\nI 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.\r\n\r\n\r\nShilpa Gupta\r\nResearch Scholar
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 08 2017 - 12:30:03 PDT
