AMBER Archive (2006)

Subject: AMBER: heme improper torsions

From: nkyx_at_sohu.com
Date: Mon Jan 16 2006 - 02:55:38 CST

Hi all,
       I am new user to Amber. When I used xleap to prepare a system containing HEME, it gave me the message enclosed. I used the parameters from http://pharmacy.man.ac.uk/amber/.
        I don't know whether the old impropers significantly affect the simulation result. Could anybody with experience give me some advice? Thanks in advance.
nkyx

The message is enclosed.
Building improper torsion parameters.
old PREP-specified impropers:
 <CYF 439>: -M CA N H
 <CYF 439>: CA +M C O
 <HEM 497>: NA C1A C4A FE
 <HEM 497>: NB C1B C4B FE
 <HEM 497>: NC C1C C4C FE
 <HEM 497>: ND C1D C4D FE
 <HEM 497>: C1A C2A NA CHA
 <HEM 497>: C1B C2B NB CHB
 <HEM 497>: C1C C2C NC CHC
 <HEM 497>: C1D C2D ND CHD
 <HEM 497>: C2A C3A C1A CAA
 <HEM 497>: C2B C3B C1B CMB
 <HEM 497>: C2C C3C C1C CMC
 <HEM 497>: C2D C3D C1D CMD
 <HEM 497>: C3A C4A C2A CMA
 <HEM 497>: C3B C4B C2B CAB
 <HEM 497>: C3C C4C C2C CAC
 <HEM 497>: C3D C4D C2D CAD
 <HEM 497>: C4A NA C3A CHB
 <HEM 497>: C4B NB C3B CHC
 <HEM 497>: C4C NC C3C CHD
 <HEM 497>: C4D ND C3D CHA
 total 1595 improper torsions applied
 22 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:
 res total affected
 CHIE 1
 NLYS 1
   (no restraint)

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