AMBER Archive (2006)

Subject: AMBER: manual/prmtop/missing bonds section

From: David Mobley (dmobley_at_gmail.com)
Date: Mon Jun 26 2006 - 15:27:39 CDT

Dear Amber users,

I need to script some editing of a prmtop file for free energy
calculations, so I have been fiddling around with using leap to
generate prmtop and crd files for methane in a very similar fashion to
that described here:
http://amber.scripps.edu/tutorial/shirts/index.html. I generate two
prmtop files: One for methane where I simply turn off the charges, and
the second where I begin with the charges turned off, and the
perturbation changes the atoms into dummy atoms.

The problem I am having (at least I think it is a problem) is that as
soon as I switch the atom types to dummy atoms, the prmtop file
sections BONDS_INC_HYDROGEN, BONDS_WITHOUT_HYDROGEN,
ANGLES_INC_HYDROGEN, and ANGLES_WITHOUT_HYDROGEN are all empty.

This occurs in both AMBER 8 and AMBER 9. The charge perturbation looks
fine, since this only occurs when I change the atoms into dummy atoms
(and yes, I have properly defined the atoms in my frcmod file and
loaded it into leap).

Any suggestions?

Maybe this is just my confusion, but if this is correct, where does
AMBER get the bond connectivity information from? I've looked at the
relevant section in the documentation but can't find much there on
what happens when perturbations are going on, although what I do see
leads me to think that I should be seeing stuff in these sections.

Thanks,
David
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