[gmx-users] Termini database for new residue type

[Justin Lemkul]

On 11/28/16 4:57 PM, Tong Xinjie wrote:
> 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

If you have one residue, are you applying multiple patches, e.g. both .n.tdb and 
.c.tdb modifications?

> 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 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 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 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 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 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 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 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.
>
> 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.


Without seeing the .rtp and .tdb entries, there's really nothing to go on here. 
Deleted atoms should trigger deletion of bonds, angles, and dihedrals.  Clearly 
something is going wrong here but there's no real way to know what it is without 
actually seeing what you're doing.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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