pdb2gmx will read in multiple .rtp files but then when trying to add terminal patches it will not find anything from the additional .rtp file for the C-terminus - Redmine #2027
Archive from user: Chris Neale
pdb2gmx will read in multiple .rtp files but then when trying to add terminal patches it will not find anything from the additional .rtp file for the C-terminus
test:
A. Use oplsaa.ff
B. Use a sequence ending in GLU
C. modify aminoacids.rtp to remove the [ GLU ] entry while new file
aminoacids_more.rtp contains the [ GLU ] entry only
Note: new file aminoacids_more.rtp also contains the same header:
[ bondedtypes ]
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14
RemoveDih
1 1 3 1 1 3 1 0
RESULT of pdb2gmx -ter:
with regular oplsaa.ff:
Select start terminus type for MET-1
0: NH3+
1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
residue)
2: NH2
3: None
0
Start terminus MET-1: NH3+
No suitable end (C or 3’) terminus found in database - assuming this
residue
is already in a terminus-specific form and skipping terminus selection.
This happens even though with the modified folder gmx pdb2gmx outputs:
Reading residue database… (oplsaa_mod)
Opening force field file
/nh/nest/u/cneale/exe/GROMACS/exec/gromacs-5.1.2/serial/share/gromacs/top/oplsaa_mod.ff/aminoacids.rtp
Residue 51
Sorting it all out…
Opening force field file
/nh/nest/u/cneale/exe/GROMACS/exec/gromacs-5.1.2/serial/share/gromacs/top/oplsaa_mod.ff/aminoacids_more.rtp
Residue 52
Sorting it all out…
There is an obvious workaround, which is to have only one .rtp file. However, if gromacs will only allow one then it should not say it is reading the other and, ideally, gromacs would either faithfully read and allow use of the other or throw an error if there is more than one.rt I have no idea why I get OK N-terminal selection but faulty C-terminal selection. The reason to desire multiple rtp files is when adding new options to an existing force field then one does not pollute the original with the addition, thus making it cleaner to share modifications without one having to test that there were no undesired additions/deletions to the file.
This might be related to issue 2026
(from redmine: issue id 2027, created on 2016-08-09 by gmxdefault, closed on 2018-01-02)
- Changesets:
- Revision 61e5b736 by Erik Lindahl on 2018-01-02T11:24:40Z:
Don't require matching names between rtp and tdb files
This was only documented in the source. It's a remnant
from the days when all force fields were in the same
directory, and no longer necessary. With this change we
will properly match all termini to all amino acids.
Fixes #2026, #2027.
Change-Id: Ie7bf8e65892281cc2744146a5525be0c4afdcecf