[gmx-users] Bug in pdb2gmx: terminal COOH in GROMOS force fields

[David van der Spoel]

On 2013-12-06 18:01, Thomas Schlesier wrote:
> Hi all,
> for the COOH terminal group one of the angles (the one including two
> carbons and the oxygen which carries the hydrogen) does not get
> overwritten by aminoacids.c.tdb.
>
> Ok, somewhat slower:
> Used ASPH as a test molecule and chose a -COOH capping group.
>
>  From aminoacids.rtp:
>
> [ ASPH ]
>   [ atoms ]
> ...
>      C     C       0.450     3
>      O     O      -0.450     3
> ...
>   [ angles ]
> ;  ai    aj    ak   gromos type
> ...
>     CA     C     O     ga_30
> ...
>
>  From aminoacids.c.tdb:
>
> [ COOH ]
> [ replace ]
> C       C       C       12.011  0.33
> O       O       OA      15.9994 -0.288
> OXT     OT      O       15.9994 -0.45
> ...
> [ angles ]
> O       C       OT      ga_33
> C       O       HO      ga_12
> CA      C       O       ga_19
> CA      C       OT      ga_30
>
> This mean that from [ASPH] the atom named O with the type O should
> exchange by an atom named O with the typ OA.
> Additionally the angle for CA-C-O should change form ga_30 to ga_19
>
> Result from pdb2gmx:
>
> ;       It was generated using program:
> ;       pdb2gmx - VERSION 4.6.5
> ;
> ;       Command line was:
> ;       pdb2gmx -f asp.pdb -o asp.gro -p asp.top -asp -ter
> ...
> ; Include forcefield parameters
> #include "gromos53a5.ff/forcefield.itp"
> ...
> [ atoms ]
> ...
>     10          C      1   ASPH      C      4      0.658     12.011   ;
>     11          O      1   ASPH     OT      4      -0.45    15.9994   ;
>     12         OA      1   ASPH      O      4     -0.611    15.9994   ;
> ...
> [ angles ]
> ...
>      4    10    11     2    ga_30
>      4    10    12     2    ga_30
> ...
>
> First line from the posted [angle] is the right angle with the atom
> named OT.
> In the second line we have still the angle from [ASPH] which doesn't get
> replaced by the angle from [COOH].
>
> I tested this with GMX 4.6.5 and GMX 4.0.7 -> Think every version from
> GMX 4.X.Y series is affected.
> Also tested it with the gromos53a5, gromos53a6, gromos43a1 force fields
> -> Think every gromos force field might be affected.
>
> Greetings
> Thomas
Thanks for reporting:

http://redmine.gromacs.org/issues/1395


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se