> In that case I wont use all the parameters. I do not have CHARMM to
> prepare
> those files.
>
> However, I imagine that the atom charges are the same, regardless of
> using
> CHARMM or Amber. Is this so?
Yes and no... The equation is the same so the charges will work. The
philosophy in fitting those charges is slightly different. AMBER works on a
per residue basis using a RESP procedure while CHARMM works on a group basis
where each group must have an integer charge. e.g. methyl groups sum to zero
charge. The electrostatic constant (the value of epsilon-R on the bottom of
the direct space charge equation) is also slightly different in the two
force fields. Couple with this the fact that things like the dihedrals are
fitted specifically with the charge model in hand and you can see how
complicated things become.
That said, is all this lost in the noise? Probably... The question to ask is
do you think you can defend your choice of parameters one way or the other.
A simple question, I as a referee or examiner would ask is, you had an
option to a) attempt to use the CHARMM parameters even though they aren't
strictly compatible but will at least work to some degree vs b) taking the
time to fit AMBER compatible parameters yourself. Why did you choose to a?
There is no simple answer to this... It is the nature of research. But for
example, if this was a residue on one side of the protein a long way from
the active site that would be a reasonable defense in itself. There might be
others such as a quick AM1-BCC resp fit showing almost no difference in the
charges, or perhaps a previous publication that used the approach you did
and showed that it did not make a difference, or maybe simulations of the
ligand in question on it's own showing it matches experiment in one way or
another etc etc.
Maybe that is more info than you wanted but I hope it helps.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
---------------------------------------------------------
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 01 2011 - 11:00:03 PDT
