Thanks Justin, I'm sorry that I'm not clear with what do you mean by "so you can likely just use the same parameters in ffbonded.itp for this dihedral in the zwitterionic form".
Also as I have mentioned before, when I look into the line 161, it refers to a dihedral term concerning (CD N CA C) which is not able to be found in ffbonded.itp. However, other dihedral terms such as (CD N CA CB) or (CD N CA HA) which are also not found in itp do not report such error and I was successful to grompp after commenting out the line 161. So why would this happen? Thanks in advance, Kevin On 2 Jun, 2015, at 20:05, Justin Lemkul <jalem...@vt.edu <javascript:_e(%7B%7D,'cvml','jalem...@vt.edu');>> wrote: On 6/1/15 12:25 PM, Kevin C Chan wrote: pdb2gmx command: gmx_d pdb2gmx -f proline.pdb -ter > 15: (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)) > 1: TIP4P TIP 4-point, recommended > 1: PRO-ZWITTERION_NH2+ (only use with zwitterions containing exactly one residue) > 1: PRO-ZWITTERION_COO- (only use with zwitterions containing exactly one residue) (I have also tried 4: ZWITTERION_NH3+ (only use with zwitterions containing exactly one residue) but the result was the same) Screen-out: http://pastebin.com/CuMa7aZ7# topology: http://pastebin.com/FSbcFGYR It appears that there are simply no parameters in the OPLS-AA force field for this entity. Whether or not this is because OPLS-AA doesn't officially have parameters for it or they are just missing from the GROMACS implementation is something you'd have to dig into, but largely it seems that all dihedral parameters for the N- and C-terminal forms of PRO are all the same, so you can likely just use the same parameters in ffbonded.itp for this dihedral in the zwitterionic form. -Justin Thanks in advance, Kevin On Tue, Jun 2, 2015 at 12:11 AM, Justin Lemkul <jalem...@vt.edu <javascript:_e(%7B%7D,'cvml','jalem...@vt.edu');>> wrote: On 6/1/15 12:09 PM, Kevin C Chan wrote: Thanks Justin, I did not but I tried just now. The aforementioned dihedral terms remain along with the errors. Please provide your full pdb2gmx command, all screen output, and full topology. Use file sharing services, pastebin, etc. as needed. -Justin Thanks in advance, Kevin On Mon, Jun 1, 2015 at 11:13 PM, Justin Lemkul <jalem...@vt.edu <javascript:_e(%7B%7D,'cvml','jalem...@vt.edu');>> wrote: On 6/1/15 10:57 AM, Kevin C Chan wrote: Dear Users, I am testing with OPLSSaa force-field of proline. First I arbitrarily extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro and top are however not suitable for further grompp (even minimization). The error messages are as follows: ERROR 1 [file topol.top, line 161]: No default Ryckaert-Bell. types When I look into the line 161, it refers to a dihedral term concerning (CD N CA C) which is not able to be found in ffbonded.itp. However, other dihedral terms such as (CD N CA CB) or (CD N CA HA) which are also not found in itp do not report such error and I was successful to grompp after commenting out the line 161. Why would this happen? Did you choose the proper "PRO-ZWITTERION-*" termini when running pdb2gmx? -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu <javascript:_e(%7B%7D,'cvml','jalem...@outerbanks.umaryland.edu');> | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org <javascript:_e(%7B%7D,'cvml','gmx-users-requ...@gromacs.org');>. -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu <javascript:_e(%7B%7D,'cvml','jalem...@outerbanks.umaryland.edu');> | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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