Hi Heather.

It doesn't sound like you have an actual "er= ror", but that MM3 simply doesn't have the non-bonded parameters t= hat your system requires.=C2=A0 I have encountered this many times when usi= ng MM3, even in what may be considered "simple" systems, e.g. an = amidoxime functional group.=C2=A0 [If you're not familiar with force fi= elds, they require certain numbers (parameters) for different "atom ty= pes."=C2=A0 Coming up with these parameters in not a trivial exercise,= especially with a force field such as MM3.=C2=A0 And for every atom type, = parameters must exist else the calculation simply cannot be performed.]

= I'm fairly familiar with MM3.=C2=A0 I don't think that peptides wer= e the focus of Allinger's work, but there may simply be some articles I= haven't read. =C2=A0

= OPLS and Merck, on the other hand, definitely focused on peptides.

=

Howe= ver, MM3 parameters are not compatible with OPLS or MMFF; MM3 has a much mo= re complex functional form.=C2=A0 So the answer will never be to simply tak= e OPLS or MMFF parameters and place them into MM3.=C2=A0 (By the way, it ma= y be worth investigating whether your software has implemented MM3 as Allin= ger intended. They wouldn't be the first to truncate some terms. Not in= any way implying that Schrodinger has done this. Just a word from experien= ce.=C2=A0 Not all "MM3"s are created equal.)

= Carefully inspect your software's MM3 parameters and make sure that you= r software isn't simply "mis-typing" the atoms.=C2=A0
If it's the case that it's correctly typing the atoms, yet is miss= ing parameters, consider using OPLS or MMFF.=C2=A0 The alternative would be= to find=C2=A0 MM3 atom types which are very similar to the ones you need a= nd having your software use those parameters instead.=C2=A0 Caveat emptor. = =C2=A0

Regards, =C2=A0

-----------------------= ------------------[00(01|10)11]----------------------------------= --------

Billy Wayne McCann, Ph.D.
Google+

PGP K= ey

ir= c://irc.freenode.net:bwayne

MzM0LTcwMy0wMTIyCg=3D=3D | base64

"A rich man will always desire what his wealth cannot acquire." ~= Faust (Goethe)

-------------------------------------= -----[11(10|01)00]---------------------= ---------------------

On Sat, Feb 8, 2014 at 10:32 AM, Heather= Shelley sh.maeam**gmail.com <owner= -chemistry#,#ccl.net> wrote:

Sent to CCL by: "Heather =C2=A0Shelley" [sh.maeam..gmail.com]
Dear All:

I am trying to submit a conformational search using macromodel
=C2=A0and the MM3 force field. The job will not run because when the progra= m
=C2=A0tries to load the parameters from the force field I get a message say= ing:
INTFFC: No nonbonded params in force field for atom type =C2=A014 (C0)
INTFFC: No nonbonded params in force field for atom type =C2=A040 (N0)
INTFFC: FFSBST fails
UPDATE_INT: INTFFC fails
MINI: Error generating interactions
BTCHMN: ERROR GENERATING INTERACTION ARRAY; ABORTING
WARNING saving minimization structure but no list entry has been set.

But the MMFFS and OPLS-2005 are fine.I look for those specific atoms listed=
above, and I can still not find the problem. BTW, The structure is protonat= ed
dipeptide.

Your help would be greatly appreciated,
Thank you,

Heather Shelley
sh.maeam[a]gmail.com
Aarhus University

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