AMBER: TI - frcmod file

From: Oliver Hucke <ohucke.u.washington.edu>
Date: Tue, 12 Jul 2005 12:21:44 -0700

Dear All,

I am setting up a TI simulation of the change of an ALA in a ligand
binding site of a protein to a GLY. The attached jpeg file shows the
changes of atom types I apply. In the process of preparing the frcmod
file for the atom type changes many errors of the following type
appeared when I tried to use my frcmod file with leap:

--- from leap output ---
*** Proper torsion parameters missing ***
  atom names: CB-CA-C-N
  atom types: CT-CT-C-N =pert=> H0-CT-C-N
Please add a dummy parameter of multiplicity 1
for the pert types to your parameter set.
  - e.g. H0-CT-C-N 1 0.0 0. 1.
(This is because multiple torsional potentials may apply to a
single torsion, and each is perturbed individually in gibbs.)
--- end of excerpt from leap output ---

After doing what leap recommended, i.e. after adding all recommended
dummy torsions to my frcmod file, everything seems to be fine, i.e. I am
able to write the prmtop and crd output files with leap. (My frcmod file
that can be used with leap without problems is also attached).
BUT: some of the dummie torsions I had to add were actually "real"
torsions defined in the force field that I am using (ff03).
For example, leap asked me to add the following dummy torsion:

H0-CT-C-N 1 0.0 0. 1.

But in frcmod.03 I find:
H0-CT-C -N 1 0.0110 0.00 -2.
H0-CT-C -N 1 1.0607 180.00 1.

Does using the dummy torsion in my frcmod file for the perturbation not
change these parameters defined in frcmod.ff03?

Thank you very much,
Oliver

-- 
________________________________________________________________
Oliver Hucke, Dr.
Biomolecular Structure Center   Health Sciences Building - K418C
Dept. of Biochemistry           1959 NE Pacific St.
University of Washington        phone: (206) 685 7046
Box 357742                      fax  : (206) 685 7002
Seattle, WA 98195-7742          email: ohucke.u.washington.edu
________________________________________________________________



# Parameters needed for the perturbation of atom types
MASS
DH 1.008 0.135

BOND
H0-DH 340.0 1.090 CT-H0
H0-DH 340.0 1.090 CT-HC

ANGLE
CT-H0-DH 50.0 109.50 CT-CT-HC
C -CT-H0 63.0 111.10 C -CT-CT
N -CT-H0 80.0 109.70 CT-CT-N
DH-H0-DH 35.0 109.50 HC-CT-HC

DIHE
X -CT-H0-X 9 1.40 0.0 3. X -CT-CT-X
H0-CT-C-N 1 0.0 0. 1. dummy requested by leap; non-dummy in frcmod.ff03
H0-CT-C-N 1 0.0 0. 2. dummy requested by leap
H0-CT-C-N 1 0.0 0. 3. dummy requested by leap
H0-CT-C-O 1 0.0 0. 1. dummy requested by leap
H0-CT-C-O 1 0.0 0. 2. dummy requested by leap
H0-CT-C-O 1 0.0 0. 3. dummy requested by leap
H1-CT-C-N 1 0.0 0. 1. dummy requested by leap
H1-CT-C-N 1 0.0 0. 2. dummy requested by leap
H1-CT-C-N 1 0.0 0. 3. dummy requested by leap
H1-CT-C-O 1 0.0 0. 1. dummy requested by leap; non-dummy in parm99.dat
H1-CT-C-O 1 0.0 0. 2. dummy requested by leap
H1-CT-C-O 1 0.0 0. 3 dummy requested by leap
C-N-CT-H0 1 0.0 0. 1. dummy requested by leap; X -CT-N -X = dummy in parm99.dat
C-N-CT-H0 1 0.0 0. 2. dummy requested by leap
C-N-CT-H0 1 0.0 0. 3. dummy requested by leap
C-N-CT-H1 1 0.0 0. 1. dummy requested by leap
C-N-CT-H1 1 0.0 0. 3. dummy requested by leap
CT-CT-C-O 1 0.0 0. 1. dummy requested by leap; X -C -CT-X = dummy in parm99.dat
CT-CT-C-O 1 0.0 0. 2. dummy requested by leap
CT-CT-C-O 1 0.0 0. 3. dummy requested by leap

IMPR

NONBON
DH 1.0000 0.000


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AtoG.jpg
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Received on Tue Jul 12 2005 - 20:53:01 PDT
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