[email protected] 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" <[email protected]>
Subject: Re: [gmx-users] No default Angle types
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
[email protected] 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
========================================
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