AMBER Archive (2005)

Subject: AMBER: prepi format and question about it

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Jul 27 2005 - 04:20:00 CDT

Dear All,

I have recalculated the RESP charges for a,c,g,u and some other unnatural
residues following the RESP protocol. I will use my derived charges for
compatibility issues in my project. I am trying to create the .lib files
for these residues. In order to do that, I am using 'antechamber' to
create the .prepi files first with the charge info given in another file.
(I will create the lib files for RX, RX3, and RX5 later)

'antechamber' assigns almost the correct atom type information
automatically, but the 4th column is different when compared with the
amber's library for those residues. (For A,C,G,and U) Do I have to change
those assigned LINK info to the ones in the AMBER database? If yes, is
there a quick way to do it?

Best,

PS: Example .prepi file

RA which is automatically created by antechamber
...
   4 O1P O2 M 3.487627 1.543250 0.125532 -0.792100
   5 P P M 2.394907 0.826000 0.819956 1.220980
   6 O2P O2 E 0.990655 1.042178 0.405519 -0.792100
   7 O5* OS M 2.703494 -0.752768 0.748009 -0.506960
...

In amber's database, the .prepi for RA is as follows:
...
   4 P P M 2.314489 1.776673 -0.478436 1.166200
   5 O1P O2 E 1.933410 3.073374 -1.081549 -0.776000
   6 O2P O2 E 3.156547 0.871841 -1.292450 -0.776000
   7 O5' OS M 2.994369 2.142475 0.922974 -0.498900
... 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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