On 3/7/13 10:46 AM, Steven Neumann wrote:
Dear Gmx Users,
I used charmm server to get the parameters for my new molecule -
alkane. i converted it into the gromacs topology.
When I try grompp:
WARNING 1 [file ffbonded.itp, line 7948]:
Overriding Proper Dih. parameters.
Use dihedraltype 4 to allow several multiplicity terms.
old: 0 0.159787 2 0 0.159787 2
new: CG331 CG321 CG321 CG331 9 0.00
0.1598288 2
WARNING 2 [file ffbonded.itp, line 7949]:
Overriding Proper Dih. parameters.
Use dihedraltype 4 to allow several multiplicity terms.
old: 0 0.159829 2 0 0.159829 2
new: CG331 CG321 CG321 CG331 9 180.00
0.1330512 6
My ffnonbonded.itp corresponding lines:
[ dihedraltypes ]
; i j k l func phi0 cp mult
CG331 CG321 CG321 CG331 9 0.00
0.1598288 2
CG331 CG321 CG321 CG331 9 180.00 0.1330512 6
Can you please explain me this? Shall use 4 instead of 2 or 6 at the
end of these lines?
No, the last entries are the multiplicity, not the function type (which is the
fifth entry, under "func"). Unfortunately, I cannot answer why grompp is
prompting you to use type 4, which according to the manual is for periodic
improper dihedrals, not proper dihedrals. Maybe you've added those lines in the
wrong directive, i.e. with impropers rather than propers?
-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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