On 5/17/12 9:47 AM, Lara Bunte wrote:
Hello
After
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
I got the error:
Incorrect number of parameters - found 2, expected 4 or 4 for U-B.
I thought that this could be an inconsistency be declaring the functions, but
in my topology I have function 4 (for improper dihedrals):
Out of topol.top
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3
1 8 6 4 4 180 100
And in my .rtp file in the CHARMM27 force field folder I have:
Out of .rtp file
; bonds angles dihedrals impropers
1 5 4 4
and in my ffbonded.itp file I have:
[ dihedraltypes ]
; i j k l func q0 cq
ON1 NN3A CN1A NN2U 4 180 100
So in alle three files, ffbonded.itp, topol.top and the .rtp parametrization
file I have the function 4 for the improper dihedrals.
What is the problem?
The U-B function type is the Urey-Bradley angle potential. It is unrelated to
dihedrals. See the [angletypes] directive of ffbonded.itp and the manual for
the proper format of U-B parameters.
-Justin
--
========================================
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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