On 3/25/20 9:04 PM, Neena Susan Eappen wrote:
Thank you Justin, but I had already defined it as C15 in atomtypes.atp for ALH (modified alanine) opls_968 12.01100 ; C15 in ALH
atomtypes.atp is irrelevant after pdb2gmx, so grompp has no knowledge of it. You need to add it to ffnonbonded.itp and include the bonded atom type (C15 in this case) as the second column so that grompp understands the translated atom type.
-Justin
________________________________ From: Neena Susan Eappen <neena.susaneap...@mail.utoronto.ca> Sent: Thursday, March 26, 2020 12:47 AM To: gromacs.org_gmx-users@maillist.sys.kth.se <gromacs.org_gmx-users@maillist.sys.kth.se> Subject: Re: [gmx-users] No default bond types I am sorry that I previously did not attach any files as I was confident how I edited. Problem Solved: By just adding those missing parameters in the topology file itself. I am showing values below for future reference: On grompp, following error came up: ERROR 1 [file topol.top, line 84]: No default bond types Line 84 in topol.top : 14 20 1 Which corresponds to a bond between CA and C15 (atoms 14 and 20) in a modified alanine residue, for which I already had parameters in the ffbonded.itp file under [ bond types] as shown below: CA C15 1 0.14900 334720.0 Problem solved by changing that line 84 in topology file Line 84: 14 20 1 0.14900 334720.0 ________________________________ From: Neena Susan Eappen <neena.susaneap...@mail.utoronto.ca> Sent: Wednesday, March 25, 2020 11:59 PM To: gromacs.org_gmx-users@maillist.sys.kth.se <gromacs.org_gmx-users@maillist.sys.kth.se> Subject: Re: [gmx-users] No default bond types Hi Justin, Yes errors from grompp are very clear. Initially, I had errors for all four 4 new bond and 9 new angle types, grompp specifically stated which line in the topology file was missing. Accordingly, I added parameters for all in the ffbonded.itp file correctly. Even after that, I still wonder why I have errors.... ________________________________ From: Neena Susan Eappen <neena.susaneap...@mail.utoronto.ca> Sent: Wednesday, March 25, 2020 8:23 PM To: gromacs.org_gmx-users@maillist.sys.kth.se <gromacs.org_gmx-users@maillist.sys.kth.se> Subject: Re: [gmx-users] No default bond types Hi Alessandra, For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp file. However, the command grompp gave error for one bond and 6 angle types although I have all in there. Is there a way to resolve this? ________________________________ From: Neena Susan Eappen Sent: Wednesday, March 25, 2020 3:17 AM To: gromacs.org_gmx-users@maillist.sys.kth.se <gromacs.org_gmx-users@maillist.sys.kth.se> Subject: [gmx-users] No default bond types Hello gromacs users, I just modified opls force field for a modified aminoacid with 4 new bond types and 9 new angle types. However, the command grompp gave a no default error for one bond and 6 angle types. Is there a way to resolve this? Many thanks and Take care, Neena
-- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
