AMBER Archive (2003)

Subject: Re: question about H-bond in carnal?

From: Bill Ross (photoriot_at_yahoo.com)
Date: Fri Apr 25 2003 - 13:57:20 CDT

> GROUP g1 ((RES 969,970,971,973)&(ATOM TYPE n? o?));

Note that every time g1 is used, either as donor or
acceptor, there is a complaint about it. Carnal has
not been updated since antechamber came out. So the
presence of antichamber lower-case atom types is a
clue.

Donor atoms have H's attached - the H's do not need to
be in the group. First, atoms with type names starting

with 'C' and 'H' are screened from the group. (C's are
allowed if the EXACT keyword is used.) This is the
first potential problem with antechamber atom types.
Then the prmtop array that lists covalent bonds
involving H's is considered. For each pair, the H is
identified by whether its type name starts with 'H' -
if the first one of the pair does not start with 'H',
it is assumed to be the heavy atom. This is the second
problem with antechamber atom types. Then the
screened group list is checked to see if the
(mis)identified heavy atom is there.

I think that the solution to this is to change the
program such that EXACT for DONOR assumes that each
atom in the group that is found in the list of
covalent bonds involving H is a heavy atom. I'll try
to make a bugfix for this over the weekend.

For acceptor, the use of EXACT with only the desired
heavy atoms should suffice.

Bill Ross
ross_at_cgl.ucsf.edu (yahoo mail checked rarely)