[gmx-users] ERROR No default G96Angle types

Fri Mar 1 22:57:07 CET 2013

On 3/1/13 3:49 PM, Villarealed wrote:
> Dear Gromacs-Users,
> I am using Gromos96 43a1 FF extended to include phosphorylated residues.
> I have a peptide-capped with 17 aminoacids.
> When I tried to add ions to the virtual box
> I obtained these error
>
> ERROR 1 [file topol.top, line 566]:
>    No default G96Angle types
> ERROR 2 [file topol.top, line 801]:
>    No default Proper Dih. types
>
> The second error  was resolved by modified the archive "residuetypes.dat".
> I only add this line "SEP     Protein"
> To be honest I don't know how to resolve the ERROR 1.
> If someone could help me I will appreciate.
> Eduardo
>
>
> grompp -f ions.mdp -c newbox_solv.gro -p topol.top -o ions.tpr
>
> ERROR 1 [file topol.top, line 566]:
>    No default G96Angle types
>
> topol.top
>
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2
> c3
>      1     2     3     2
>
> newbox_solc.gro
>      1ACE     CA    1   2.759   1.040   1.830
>      1ACE      C    2   2.881   1.130   1.839
>      1ACE      O    3   2.988   1.083   1.878
>      2SER      N    4   2.872   1.258   1.805
>
> aminoacids.rtp
> [ ACE ]
>   [ atoms ]
>      CA   CH3   0.000     0
>       C     C   0.380     1
>       O     O  -0.380     1
>   [ bonds ]
>       C    CA   gb_26
>       C     O   gb_4
>       C    +N   gb_9
>   [ angles ]
>     CA     C    +N    ga_18
>      O     C    +N    ga_32
>   [ impropers ]
>      C    CA    +N     O    gi_1
>

It looks like you are using an old version of Gromacs.  This was a bug that was 
fixed some time ago.  There is a missing angle here:

    CA     C     O    ga_30

> ERROR 2 [file topol.top, line 801]:
>    No default Proper Dih. types
>
> topol.top
> [ dihedrals ]
> ;  ai    aj    ak    al funct            c0            c1            c2
> c3            c4            c5
>     72    71    73    74     1
>     H     N     CA    CB

There should not be a dihedral assigned here.  It is not specified in the .rtp, 
nor do the Gromos force fields assign dihedrals for H-N-X-X.  The -N-CA- torsion 
is defined by heavy atoms only.  Are you sure the numbering is correct?  The 
numbers listed in topol.top correspond to the [moleculetype] numbering, which is 
not necessarily the same numbering in the coordinate file, if (for example) the 
residue/atom numbering does not start at 1 in the coordinate file.

-Justin

> newbox_sol.gro
>     10SEP      N   71   2.348   2.562   2.883
>     10SEP      H   72   2.446   2.556   2.863
>     10SEP     CA   73   2.260   2.594   2.768
>     10SEP     CB   74   2.186   2.467   2.720
>     10SEP     OG   75   2.110   2.424   2.827
>     10SEP      P   76   2.001   2.314   2.797
>     10SEP    O1P   77   2.066   2.200   2.732
>     10SEP    O2P   78   1.949   2.275   2.928
>     10SEP    O3P   79   1.895   2.372   2.710
>     10SEP      C   80   2.164   2.714   2.789
>     10SEP      O   81   2.051   2.714   2.741
>
> aminoacids.rtp
> [ SEP ]tar -zcvf prog-1-jan-2005.tar.gz /home/jerry/prog
>   [ atoms ]
>      N     N    -0.28000     0
>      H     H     0.28000     0
>     CA   CH1     0.00000     1
>     CB   CH2     0.00000     2
>     OG    OA    -0.36000     2
>      P     P     0.94000     2
>    O1P    OP    -0.86000     2
>    O2P    OP    -0.86000     2
>    O3P    OP    -0.86000     2
>      C     C       0.380     3
>      O     O      -0.380     3
>   [ bonds ]
>      N     H    gb_2
>      N    CA    gb_20
>     CA     C    gb_26
>      C     O    gb_4
>      C    +N    gb_9
>     CA    CB    gb_26
>     CB    OG    gb_17
>     OG     P    gb_27
>      P   O1P    gb_23
>      P   O2P    gb_23
>      P   O3P    gb_23
>   [ angles ]
> ;  ai    aj    ak   gromos type
>     -C     N     H     ga_31
>      H     N    CA     ga_17
>     -C     N    CA     ga_30
>      N    CA     C     ga_12
>     CA     C    +N     ga_18
>     CA     C     O     ga_29
>      O     C    +N     ga_32
>      N    CA    CB     ga_12
>      C    CA    CB     ga_12
>     CA    CB    OG     ga_12
>     CB    OG     P     ga_25
>     OG     P   O1P     ga_13
>     OG     P   O2P     ga_13
>     OG     P   O3P     ga_13
>    O1P     P   O2P     ga_28
>    O1P     P   O3P     ga_28
>    O2P     P   O3P     ga_28
>   [ impropers ]
> ;  ai    aj    ak    al   gromos type
>      N    -C    CA     H     gi_1
>      C    CA    +N     O     gi_1
>     CA     N     C    CB     gi_2
>   [ dihedrals ]
> ;  ai    aj    ak    al   gromos type
>    -CA    -C     N    CA     gd_4
>     -C     N    CA     C     gd_19
>      N    CA     C    +N     gd_20
>      N    CA    CB    OG     gd_17
>     CA    CB    OG     P     gd_14
>     CB    OG     P   O1P     gd_11
>
>
>
>
>
> -----
> Eduardo Villarreal Ramírez
> Postdoctoral Research Fellow
> Mineralized Tissue Laboratory,
> Hospital for Special Surgery.
>
>
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/ERROR-No-default-G96Angle-types-tp5006044.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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