[gmx-users] Problem with adding New peptide Terminus

[Neena Susan Eappen]

Hi Justin,

This is the actual error message,

Residue 3 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom C used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.

I was trying to add a modified C-terminus for my peptide, an amide group at the C-terminus with a protonated carbonyl oxygen,  formula here [https://r2.res.outlook.com/owa/prem/images/photo_16x16.png] C_Terminus.png<https://utoronto-my.sharepoint.com/personal/neena_susaneappen_mail_utoronto_ca/_layouts/15/onedrive.aspx?id=%2Fpersonal%2Fneena%5Fsusaneappen%5Fmail%5Futoronto%5Fca%2FDocuments%2FC%5FTerminus%2Epng&parent=%2Fpersonal%2Fneena%5Fsusaneappen%5Fmail%5Futoronto%5Fca%2FDocuments&originalPath=aHR0cHM6Ly91dG9yb250by1teS5zaGFyZXBvaW50LmNvbS86aTovZy9wZXJzb25hbC9uZWVuYV9zdXNhbmVhcHBlbl9tYWlsX3V0b3JvbnRvX2NhL0VXdEFoTWRqWHF4Q2hHUlpYV083eWpBQkh0eVdVdy1LQUxtanpINWlIR3BFY0E_cnRpbWU9clF6QkZveEMxMGc>

This is the content of my PDB file
[https://r1.res.outlook.com/owa/prem/images/txt_16x16.png]PDBcontent.txt<https://utoronto-my.sharepoint.com/:t:/g/personal/neena_susaneappen_mail_utoronto_ca/EaBgTX45S9ZCv3Kn0br_-eoBdMP5dP_mGFQWVBKy9qofuw?email=gromacs.org_gmx-users%40maillist.sys.kth.se&e=r0P5af>

I edited the tdb.c in the following way (no change in the aminoacid.rtp file)

[ protonatedamide ]
[ replace ]
C CT5 opls_968 12.011   0.641
O O1  opls_967 15.9994 -0.188
[ add ]
1 1 NT CT5 O1           CA
             opls_237 14.0067   -0.76
2 3 HT NT CT5 CA
             opls_240  1.008       0.38
1 2 HO1 O1 CT5 CA
              opls_966 1.008       0.547
[ bonds ]
HO1        O1
NT           CT5
HT           N

Thank you for your time,
Neena


________________________________
From: Neena Susan Eappen
Sent: Tuesday, September 24, 2019 1:48 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Problem with adding New peptide Terminus

Hello gromacs users,

I was trying to add a modified C-terminus for my peptide, an amide group at the C-terminus with a protonated carbonyl oxygen,  formula here [https://r2.res.outlook.com/owa/prem/images/photo_16x16.png] C_Terminus.png<https://utoronto-my.sharepoint.com/:i:/g/personal/neena_susaneappen_mail_utoronto_ca/EWtAhMdjXqxChGRZXWO7yjABHtyWUw-KALmjzH5iHGpEcA>

I edited the tdb in the following way

[ protonatedamide ]
[ replace ]
C CT5 opls_968 12.011   0.641
O O1  opls_967 15.9994 -0.188
[ add ]
1 1 NT CT5 O1           CA
             opls_237 14.0067   -0.76
2 3 HT NT CT5 CA
              opls_240 1.008       0.38
1 2 HO1 O1 CT5 CA
              opls_966 1.008       0.547
[ bonds ]
HO1        O1
NT           CT5
HT           N

I got an error message saying C atom in the input file does not correspond to topology database.
I do not understand why I got this error message.
Please let me know where I am going wrong.

Thank you,
Neena