[gmx-users] Termini database for new residue type

Mon Nov 28 22:58:50 CET 2016

Hi all,

It's a new type of residue I created. I need to delete a couple of atoms and add one H back as one termini. But I don't know how to delete angles and dihedrals in tdb file for those involved atoms. Atoms deleted in termini database seems not to be ignored for angles or dihedrals since pdb2gmx are still searching for them.

pdb2gmx -f pca.pdb -ter -v

Deleting atom 'H1' in residue 'PCA' 0
Deleting atom 'O' in residue 'PCA' 0
Deleting atom 'C1' in residue 'PCA' 0
Deleting atom 'C2' in residue 'PCA' 0
Deleting atom 'H4' in residue 'PCA' 0
Deleting atom 'C5' in residue 'PCA' 0
Deleting atom 'H6' in residue 'PCA' 0
Deleting atom 'O3' in residue 'PCA' 0
Deleting atom 'H7' in residue 'PCA' 0
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 23 atoms
Making bonds...
Number of bonds was 32, now 20
Generating angles, dihedrals and pairs...

WARNING: WARNING: Residue 1 named PCA of a molecule in the input file was mapped
to an entry in the topology database, but the atom H1 used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 1 named PCA of a molecule in the input file was mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 1 named PCA of a molecule in the input file was mapped
to an entry in the topology database, but the atom C1 used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 1 named PCA of a molecule in the input file was mapped
to an entry in the topology database, but the atom H4 used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 1 named PCA of a molecule in the input file was mapped
to an entry in the topology database, but the atom C2 used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 1 named PCA of a molecule in the input file was mapped
to an entry in the topology database, but the atom H6 used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 1 named PCA of a molecule in the input file was mapped
to an entry in the topology database, but the atom C5 used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 1 named PCA of a molecule in the input file was mapped
to an entry in the topology database, but the atom H1 used in
an interaction of type dihedral in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 1 named PCA of a molecule in the input file was mapped
to an entry in the topology database, but the atom O used in
an interaction of type dihedral in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 1 named PCA of a molecule in the input file was mapped
to an entry in the topology database, but the atom C1 used in
an interaction of type dihedral in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 1 named PCA of a molecule in the input file was mapped
to an entry in the topology database, but the atom C2 used in
an interaction of type dihedral in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

Before cleaning: 29 pairs

-------------------------------------------------------
Program pdb2gmx, VERSION 5.0.4
Source code file: /home/bnovak1/installed/gromacs-5.0.4/src/gromacs/gmxpreprocess/pgutil.c, line: 125

Fatal error:
Residue 1 named PCA of a molecule in the input file was mapped
to an entry in the topology database, but the atom C2 used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

Termini database for new residue tye - ResearchGate. Available from: https://www.researchgate.net/post/termini_database_for_new_residue_tye [accessed Nov 28, 2016].
[https://i1.rgstatic.net/ii/profile.image/AS%3A433500349308936%401480365945477_l/Xinjie_Tong.png]<https://www.researchgate.net/post/termini_database_for_new_residue_tye>

Termini database for new residue tye<https://www.researchgate.net/post/termini_database_for_new_residue_tye>
www.researchgate.net
It's a new type of residue I created. I need to delete a couple of atoms and add one H back as one termini. But I don't know how to delete angles and dihedrals in tdb for those involved...