AMBER Archive (2005)

Subject: AMBER: some questions when using ATP

From: du yongchun (phoebus2008_at_hotmail.com)
Date: Wed Oct 26 2005 - 21:28:44 CDT


hi,amber
    I have some questions when using ATP in amber8.I download atp prep &=20
 frcmod files in http://pharmacy.man.ac.uk/amber/,and then use them in=20
 tleap.The command is as following:
 source leaprc.gaff
 mods=3Dloadamberparams frcmod.phos(downloaded)
  loadamberprep ATP.prep(downloaded)
  x=3Dsavepdb atp atp.pdb
But when I use VMD to see the atp.pdb ,I find the there are not bonds=20
 between phoshate groups. Can you tell me why and how I modify them.
Thanks ! =20
                                           du
                                           2005.6.2

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