[gmx-users] No default Angle types
Justin A. Lemkul
jalemkul at vt.edu
Tue May 12 00:23:30 CEST 2009
darrellk at ece.ubc.ca wrote:
> Dear All,
> I ran grompp and was presented with the following error:
> ERROR 0 [file "graphene_nm_test.top", line 51217]:
> No default Angle types
> Line 51217 of the topology file is:
> 5116 5115 5117 1
> and atoms 5115 to 5117 are defined in the topology file as:
> 5115 opls_145 1 Grph C 4859 -0.12 12.011 ;
> qtot -0.12
> 5116 opls_146 1 Grph H 4859 0.06 1.008 ;
> qtot -0.06
> 5117 opls_146 1 Grph H 4859 0.06 1.008 ;
> qtot 0
> My assumption is that this error means that there does not exist an
> angletype for this threesome of atoms in the ffolpsaabon.itp file.
You are correct. Take a closer look at the atom types:
opls_145 12.01100 ; Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl
opls_146 1.00800 ; Benzene H - 12 site.
Both atom types correspond to benzene/aromatic sites. So, in these aromatic
species, there is no such thing as a ring CH2.
Maybe you want something more like:
opls_136 12.01100 ; alkane CH2
opls_140 1.00800 ; alkane H.
> I looked within the ffoplsaabon.itp file for an entry of the form:
> HA CA HA
> and, as expected, "pattern not found" was returned as the response.
> So, I copied over the ffoplsaabon.itp file to my home (working) directory
> and added the following test entry:
> HA CA HA 1 107.000 276.000 ; TEST PARAMETERS *****
> NOT VALID *** ONLY FOR TESTING
> I expected that the ERROR O message above would disappear. But the error
> was still present. Could you please tell me what I need to do in order
> to resolve this error?
> Much thanks in advance.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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