[gmx-users] No default Angle types

[Justin A. Lemkul]

darrellk at ece.ubc.ca wrote:
> 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?
> 

I don't know, but probably.  x2top is under continual development, and does not 
always work as expected.  One way you might hack it is to define some fictitious 
atom X for every aromatic H you have (so in the .n2t file and the .pdb, 
substitute the H atom for X, e.g.) - you might be dealing with some weird atom 
names, but the atom types will all be correct.

I don't know if that will work, but it's something to try.

-Justin

> 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
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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

========================================