AMBER Archive (2008)

Subject: AMBER: Nonbonded FE parameter missing in frcmod.

From: moitrayee_at_mbu.iisc.ernet.in
Date: Thu Sep 11 2008 - 07:22:58 CDT

Dear Amber Users,

I am trying to simulate a protein having [3fe-4s]+1 as a ligand. I have
generated the prep files for it and when i am doing parmchk i get the following
.frcmod file:
remark goes here
MASS
S 32.060 2.900 same as ss
FE 55.000 0.000 ATTN, need revision

BOND

ANGLE

DIHE

IMPROPER

NONBON
  S 2.0000 0.2500 same as ss
  FE 0.0000 0.0000 ATTN, need revision

The above values are absent from parm99.dat. What should i do? Also i saw in a
paper doing simulation using charmm that the nonbonded terms can be damped using
the switch function for van der Waal's terms and a shifted function for
electrostatics at 12 angstroms. What does this mean? I would be grateful if
anybody can give me an idea what to do.
Thanks a lot in advance.
Sincere Regards,
Moitrayee Bhattacharyya
Molecular Biophysics Unit,
Indian Institute of Science.
Bangalore- 560 012
India. 

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