

AMBER Archive (2007)Subject: RE: AMBER: frcmod file From: Ross Walker (ross_at_rosswalker.co.uk)Date: Wed Apr 18 2007  10:51:20 CDT
Dear Deepti,
> since dehydrophenylalanine is a non standard residue so i editted it
Note the double bond etc in leap is used only for display purposes and if
>, now i need to set the angle between
The file format is described here: http://amber.scripps.edu/formats.html
Note there is no PN in an angle specification so I don't know what you mean
ITT , JTT , KTT , TK , TEQ
FORMAT(A2,1X,A2,1X,A2,2F10.2)
So a suitable example would be:
CTCTHC 50.0 109.5
So the angle force constant is 50.0 and the equilibrium angle is 109.5
For dihedrals the format is:
IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
This is for the equation:
Edih = V/2 (1+cos[n * phi  gamma])
PK is V/2, Phase is gamma and PN is n.
IDIVF can be a little confusing here. This is the number of combinations of
X  CT  CT  X
There are 9 dihedral terms here so IDIVF would be 9. My advice is to never
> also i need to make two structures each with
Your best bet here would be to use restraints to for the angles during MD
Ross
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