On 3/25/13 2:37 AM, Emanuel Birru wrote:
Hi Jeremy,
I am not an expert of amber ff, but what I have notice form the ffbonded.itp
file of amber99sb is that it does not have an improper header and it might use
dihedraltypes for both proper and improper; or constratinttypes. It would be
good to get a comment from someone who knows how amber works well.
The directive is [dihedraltypes]. One can differentiate between propers and
impropers by looking at the function type (see Table 5.5 in the manual).
Another problem might be with your atom names ( CAD OAX CAB CAG ) . If the
atom names of your ligand are not available in the amber99sb ff, when you
generate your top/itp file it wont understand them. If you want include new
atom/molecule it is always good to get the parameters from some other
literature or use the very similar kind of atoms to generate an itp and check
whether your parameters are good or bad by calculating some other
physicochemical property.
Atom names are not what ffbonded.itp uses. Interaction types are defined by
atom types.
-Justin
By the way, you can include your atom/molecules or new parameters in general in
amber99sb or any force field and generate you're an itp file for your new
molecules. But you have to be careful not to mess up other parts of the ff. Or
you can create your own copy and incorporate in the simulation package (top
folder).
It would be good if you explain what you are trying to do in detail to get more
productive help.
Cheers,
EB
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Yongliang Yang
Sent: Monday, 25 March 2013 5:01 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] (no subject)
Dear EB,
Many thanks for the kind reply! We have revised the improper section followed your
advice. The force field is amber99sb. Unfortunately, the program complained again,
"No default proper dih. types'. Any advice?
Thanks!
Cheers
Jeremy
---------------
Hi Jeremy,
I have checked how improper dihedral should look like in Amber, guessing that
you used amber99sb force field. But I am wondering from where the improper in
your ligand.itp was generated. As it doesn not look alike with the amber force
field. It actually is not the problem of multiplicity but the number of
parameters that you put in the improper is not enough. It should be at least
three parameters in the improper section
Yours look like
[ impropers ]
CAD OAX CAB CAG 0.000 167.4 (two parameters here angle and
force constant)
Whereas the program is looking for
CT CT OS CT 9 0.0 1.60247 3 (here function, angel,
force constant and multiplicity??) copied from the amber bonded force field
parameter :)
I think you should generate a logical itp file which fullfil all the necessary
requirements before you run you simulation.
Cheers,
EB
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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