as you can see no angle of type c3-o-s6 is provided. Is it some bug or am i
doing something wrong?
Hi Amit
When a bond-type, angle-type, or dihedral-type is missing in one of
the standard force-fields included with moltemplate (such as AMBER or
OPLSAA), it usually means that one of your atom times is incorrect.
In your case, the culprit appears to be "o". The "o" atom type is
described as "Oxygen with one connected atom" (gaff.lt, line 101). I
think you should choose "os" ("Ether and ester oxygen").
Incidentally, there is an angle defined between c3-os-s6 ("gaff.lt,
line 4734)
Figuring out the nomenclature used for each atom type can be a
headache, and it is force-field specific. I assume that graphical
molecule builders which are familiar with the different force-fields
may choose or suggest atom types based on the context where the atoms
appear. Moltemplate does not do that. You must read the atom type
descriptions, and choose the atom types carefully. Fortunately, when
you make a mistake, usually moltemplate will let you know indirectly,
as it did here. It's good that you noticed the problem. (Some users
are not so careful.)
Incidentally, non-zero net charge is another common symptom which
occurs when the user makes a mistake in the atom type:
http://lammps.sandia.gov/threads/msg50912.html
Unfortunately, this only occurs with force-fields which assign
atomic charge purely according to atom type (such as OPLS).
--- Details ---
There is no c3-o-s6 angle interaction in gaff.lt because this
interaction does not appear in the list of angle interactions in
gaff.dat distributed with AmberTools. You can find an old version of
that particular file here:
http://archive.ambermd.org/201111/att-0689/gaff.dat
(Incidentally, if you're curios, the "gaff.lt" file is generated
automatically directly from the "gaff.dat" file by the
"amberparm2lt.sh" script in the "moltemplate/common/amber/"
subdirectory. If a newer version of gaff.dat is released, you can
update "gaff.lt" using that script, in case I forget to update it.)
--- Charge ---
Since I brought up charge, I want to add a warning about another
limitation of moltemplate: Moltemplate does not do quantum chemistry.
With AMBER/GAFF, the atomic partial charges are set to zero by
default. AMBER users typically use the free AmberTools program to
perform a quantum-chemistry calculation which will determine atomic
charges. After doing that, they must add them in by hand later by
editing the "Data Atoms" section of each .LT which defines a molecule
and assigning partial charge to each atom (before running
moltemplate.sh). (Charge is located in the 4th column.) If anyone
has any suggestions, how to make this easier, I'd love to hear them.
An alternative option which is much less work is to lookup the
charges according to OPLS conventions. You can find these in the
"charge" and "atom" sections of the oplsaa.prm file available here:
http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
The OPLSAA force field contains a very large number of atom types.
Many atom types differ only by their partial charge. Once you figure
out which OPLSAA atom types correspond to the atoms in your molecule,
then you can modify the "Data Atoms" sections of your .LT files
accordingly (as explained above). I suspect the AmberTools approach
is probably more accurate, but I've seen people do both.
I hope this helps
Andrew
P.S.
If you get the SDS example working, I'd love to include it in the
moltemplate examples. If that's okay with you, feel free to send it
to me. (I like examples.) Cheers.