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" <[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 >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >-- >======================================== > >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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
