AMBER Archive (2007)

Subject: AMBER: heme force-field (2)

From: john chen (johnchen51_at_gmail.com)
Date: Tue Sep 11 2007 - 10:08:05 CDT

Dear amber experts,

Having asked about atom types, I subsequently realised that atoms NP, NO and
CX are
defined in parm94.dat but not in parm99.dat...

all I did was change in parm99.dat the original:

  HW OW 0000. 0000. 4. flag for fast
water

N NA N2 N* NC NB NT NY
C* CA CB CC CD CK CM CN CQ CR CV CW CY CZ

MOD4 RE

to this:

  HW OW 0000. 0000. 4. flag for fast
water

N NA N2 N* NC NB NT NY NP NO
C* CA CB CC CD CK CM CN CQ CR CV CW CX CY CZ

MOD4 RE

On rerunning the script, at the saveamberparm command, I now get the output
below.
Are the topology files and coordinate files OK now, or is there something
else that I have to change
in parm99.dat?

I appologise for the last email.

with best regards,
JC.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
 <HEM 89>: NA C1A C4A FE
 <HEM 89>: NB C1B C4B FE
 <HEM 89>: NC C1C C4C FE
 <HEM 89>: ND C1D C4D FE
 <HEM 89>: C1A C2A NA CHA
 <HEM 89>: C1B C2B NB CHB
 <HEM 89>: C1C C2C NC CHC
 <HEM 89>: C1D C2D ND CHD
 <HEM 89>: C2A C3A C1A CAA
 <HEM 89>: C2B C3B C1B CMB
 <HEM 89>: C2C C3C C1C CMC
 <HEM 89>: C2D C3D C1D CMD
 <HEM 89>: C3A C4A C2A CMA
 <HEM 89>: C3B C4B C2B CAB
 <HEM 89>: C3C C4C C2C CAC
 <HEM 89>: C3D C4D C2D CAD
 <HEM 89>: C4A NA C3A CHB
 <HEM 89>: C4B NB C3B CHC
 <HEM 89>: C4C NC C3C CHD
 <HEM 89>: C4D ND C3D CHA
 total 364 improper torsions applied
 20 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

        CALA 1
        NALA 1

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