Interesting, I did have that line in ffnonbonded.itp opls_968 C15 6 12.01100 0.641 A 3.55000e-01 3.17984e-01 ________________________________ From: Neena Susan Eappen <neena.susaneap...@mail.utoronto.ca> Sent: Thursday, March 26, 2020 1:04 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
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 ________________________________ 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 -- 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.
