[gmx-users] No default Angle types
Justin A. Lemkul
jalemkul at vt.edu
Tue May 12 13:22:17 CEST 2009
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
> 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
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.
> Much thanks in advance.
>> 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.
>>> 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
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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