[gmx-users] Problem with adding New peptide Terminus

[Justin Lemkul]

On 9/26/19 10:26 AM, Neena Susan Eappen wrote:
> 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 can't access the text of the PDB file because it requires a passcode 
that will be sent to the entire mailing list.

The error suggests that you simply don't have an atom named "C" in the 
terminal residue to which the patching is being applied. Check to make 
sure you do and rename as appropriate.

-Justin

> 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

-- 
==================================================

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

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================