[gmx-users] No default Angle types

[darrellk at ece.ubc.ca]

Hi Justin,
Thanks for the quick reply.

Yes, I was also thinking about using a different atom type such as the
alkane types you mentioned below. However, when I thought about how I
can include these atom types in my .n2t file, I recognized that this
might cause a potential problem since now I would have two definitions
for an H atom, as I would then have one definition for an H atom
attached to a C atom within a benzene ring and another definition for an
H atom attached to a C atom that is not on a benzene ring. Thus, my .n2t
file would then look as follows:

C    opls_145    0      12.011  3    C 0.140   C 0.140   C 0.140
C    opls_145    -0.06  12.011  3    C 0.140   C 0.140   H 0.108
H    opls_146    0.06    1.008  1    C 0.108 (H attached to benzene ring)
C    opls_136    -0.12  12.011  3    C 0.140   H 0.108   H 0.108
H    opls_140    0.06    1.008  1    C 0.108 (H not attached to benzene
ring)

Would this dual definition of the H atom confuse GROMACS? Would GROMACS
know when to use the opls_146 definition and when to use the opls_140
definition?

Much thanks in advance.

Darrell

>Date: Mon, 11 May 2009 18:23:30 -0400
>From: "Justin A. Lemkul" <jalemkul at vt.edu>
>Subject: Re: [gmx-users] No default Angle types
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4A08A562.5020809 at vt.edu>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
>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.
>
>-Justin
>
>> 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.
>>
>> Darrell
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>
>--
>========================================
>
>Justin A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin