AMBER Archive (2009)

Subject: [AMBER] Non-Standard Atoms

From: Jack Shultz (js_at_drugdiscoveryathome.com)
Date: Sat Dec 19 2009 - 19:56:28 CST

First, I seem to get an error when I open tleap: frcmod.ff99SB not found.
Where can I find this file, moreover is it needed for what I am doing?
I'm preping a structure for analysis. It also says 588 atoms not in
residue templates. How can I report on which atoms? Can I make leap
ignore these atoms?

tleap -s -f /usr/local/antechamber-1.27/dat/leap/cmd/leaprc.ff99SB
-I: Adding /usr/local/antechamber-1.27/dat/leap/prep to search path.
-I: Adding /usr/local/antechamber-1.27/dat/leap/lib to search path.
-I: Adding /usr/local/antechamber-1.27/dat/leap/parm to search path.
-I: Adding /usr/local/antechamber-1.27/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source /usr/local/antechamber-1.27/dat/leap/cmd/leaprc.ff99SB.

Welcome to LEaP!
Sourcing: /usr/local/antechamber-1.27/dat/leap/cmd/leaprc.ff99SB
Log file: ./leap.log
Loading parameters: /usr/local/antechamber-1.27/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Could not open file frcmod.ff99SB: not found
Loading library: /usr/local/antechamber-1.27/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/antechamber-1.27/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/antechamber-1.27/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/antechamber-1.27/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/antechamber-1.27/dat/leap/lib/ions94.lib
Loading library: /usr/local/antechamber-1.27/dat/leap/lib/solvents.lib

...
Created a new atom named: HN within residue: .R<CARG 275>
  total atoms in file: 3844
  Leap added 608 missing atoms according to residue templates:
       608 H / lone pairs
  The file contained 588 atoms not in residue templates 

-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org

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