[gmx-users] No default Proper Dih. types when using neutral terminal

[Mark Abraham]

Hi,

I would look back to the literature to find what terminal PRO has CMAP
defined.

Mark

On Thu, 26 Oct 2017 16:10 Simon Kit Sang Chu <simoncks1994 at gmail.com> wrote:

> Hi everyone,
>
> Last time, I mentioned missing parameter for neutral terminal dihedral and
> U-B type. After some debugging, I am still not sure what the cause was. I
> hope providing more information could help to resolve the issue. I am using
> CHARMM36 forcefield.
>
> Brief summary of the problem -
> No dihed. parameter / U-B types after using neutral terminals
>
> Command I ran -
>
>    1. gmx pdb2gmx -f ALA-GLY-GLY-PRO. pdb -o ALA-GLY-GLY-PRO.gro -p
>    ALA-GLY-GLY-PRO.top -i ALA-GLY-GLY-PRO.itp -water tip3p -ignh -ter
>    Choose CHARMM36 all-atom force field (November 2016), NH2 and COOH
>    terminals
>    2. gmx editconf -f ALA-GLY-GLY-PRO.gro -o ALA-GLY-GLY-PRO-box.gro -c -d
>    0.8 -bt dodecahedron
>    3. gmx solvate -cp ALA-GLY-GLY-PRO-box.gro -cs spc216.gro -o
>    ALA-GLY-GLY-PRO-solvated.gro -p ALA-GLY-GLY-PRO.top
>    4. gmx grompp -f ions.mdp -c ALA-GLY-GLY-PRO-solvated.gro -p
>    ALA-GLY-GLY-PRO.top -o ions.tpr
>
> Fatal error in grompp -
>
>
> ERROR 1 [file ALA-GLY-GLY-PRO.top, line 293]:
>   No default U-B types
>
> ERROR 2 [file ALA-GLY-GLY-PRO.top, line 367]:
>   No default Proper Dih. types
>
> Meanwhile in the topology file -
>
> [ angles ]
>
>    30    38    40     5          ( line 293 )
>
>
> [ dihedral ]
>
>    27    26    30    38     9  ( line 367 )
>
> ; residue   5 PRO rtp PRO  q  0.0
>     26          N      5    PRO      N     26      -0.29     14.007   ;
> qtot -0.29
>     27        CP3      5    PRO     CD     27          0     12.011   ;
> qtot -0.29
>     28        HA2      5    PRO    HD1     28       0.09      1.008   ;
> qtot -0.2
>     29        HA2      5    PRO    HD2     29       0.09      1.008   ;
> qtot -0.11
>     30        CP1      5    PRO     CA     30       0.02     12.011   ;
> qtot -0.09
>     31        HB1      5    PRO     HA     31       0.09      1.008   ;
> qtot 0
>     32        CP2      5    PRO     CB     32      -0.18     12.011   ;
> qtot -0.18
>     33        HA2      5    PRO    HB1     33       0.09      1.008   ;
> qtot -0.09
>     34        HA2      5    PRO    HB2     34       0.09      1.008   ;
> qtot 0
>     35        CP2      5    PRO     CG     35      -0.18     12.011   ;
> qtot -0.18
>     36        HA2      5    PRO    HG1     36       0.09      1.008   ;
> qtot -0.09
>     37        HA2      5    PRO    HG2     37       0.09      1.008   ;
> qtot 0
>     38         CD      5    PRO      C     38       0.72     12.011   ;
> qtot 0.72
>     39         OB      5    PRO    OT1     39      -0.55    15.9994   ;
> qtot 0.17
>     40        OH1      5    PRO    OT2     40      -0.61    15.9994   ;
> qtot -0.44
>     41          H      5    PRO    HT2     41       0.44      1.008   ;
> qtot 0
>
>
> I further check if angle type between CP1, CD and OH1 exists in ffbond.itp.
> Indeed there is no such angle.  Maybe there is something wrong when using
> NH2 and COOH terminals?
>
> Please feel free to give any suggestion. I appreciate any comment.
>
> Regards,
> Simon
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