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
> manually in xleap. i added a double bond between alpha carbon and beta
> carbon and did necessary changes.

Note the double bond etc in leap is used only for display purposes and if
you ask leap to add the hydrogens to the template you are building it has no
effect on the prmtop and inpcrd files that are written. Here there is no
concept of a double bond...

>, now i need to set the angle between
> alpha carbon and beta carbon to 0 degrees. when i look at frcmod file
> which could be loaded in xleap to make necessary changes, i do not
> understand its format. what is PN number there?

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
here. The format for Angles in an frcmod file is:

ITT , JTT , KTT , TK , TEQ

                        FORMAT(A2,1X,A2,1X,A2,2F10.2)

So a suitable example would be:

CT-CT-HC 50.0 109.5

So the angle force constant is 50.0 and the equilibrium angle is 109.5
degrees. These are the parameters for the equation: Eangle =
K(theta-thetaeq). 50.0 is K and 109.5 is theta eq.

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
this dihedral. It only makes sense when you have wild cards e.g.

X - CT - CT - X

There are 9 dihedral terms here so IDIVF would be 9. My advice is to never
use wild cards and always set this to 1 and specify the barrier height for
an individual dihedral.

> also i need to make two structures each with
> PSI= PHI=180 and chi =0
>
> and the other is PSI=PHI=-180 and chi=0

Your best bet here would be to use restraints to for the angles during MD
rather than trying to build the input structures directly in Leap.
 
Good luck...

Ross

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|\oss Walker

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| San Diego Supercomputer Center |
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