[gmx-users] Problems with PHL in ffgmx.rtp

[David]

On Fri, 2004-10-15 at 15:44, Sean Cory wrote:
> Hi,
> I ran a simulation with a PHL residue and I noticed there was no bond between 
> the HY and OY atoms. 
> When looking at ffgmx.rtp I noticed that in the bonds list there was a HY1 OY 
> bond. There is no HY1 in the atoms list. When HY1 is changed to HY it seems 
> to work fine.
> I'm new to gromacs, does anybody see anything wrong with the change? Is this 
> the right thing to do?
Looks fine with me. Maybe you want to do this in a better force field?
> 
> Sean Cory
> McGill
> 
> 
> 
> This is the original PHL entry in ffgmx.rtp
> 
> [ PHL ]
>  [ atoms ]
>      N     N  -0.280     0
>      H     H   0.280     0
>     CA   CH1   0.000     1
>     CB   CH2   0.000     2
>     CG    CB   0.000     3
>    CD1   CR6  -0.140     4
>    HD1   HCR   0.140     4
>    CD2   CR6  -0.140     5
>    HD2   HCR   0.140     5
>    CE1   CR6  -0.140     6
>    HE1   HCR   0.140     6
>    CE2   CR6  -0.140     7
>    HE2   HCR   0.140     7
>     CZ   CR6  -0.140     8
>     HZ   HCR   0.140     8
>     CX   CH2   0.150     9
>     OY    OA  -0.548     9
>     HY    HO   0.398     9
>  [ bonds ]
>      N     H
>      N    CA
>     CA     CX
>     CX     OY
>     HY1     OY
>     -C     N
>     CA    CB
>     CB    CG
>     CG   CD1
>     CG   CD2
>    CD1   HD1
>    CD1   CE1
>    CD2   HD2
>    CD2   CE2
>    CE1   HE1
>    CE1    CZ
>    CE2   HE2
>    CE2    CZ
>     CZ    HZ
>  [ impropers ]
>      N    -C    CA     H
>     -C   -CA     N    -O
>     CA     N     C    CB
>     CG   CD1   CD2    CB
>    CD2    CG   CD1   CE1
>    CD1    CG   CD2   CE2
>     CG   CD1   CE1    CZ
>     CG   CD2   CE2    CZ
>    CD1   CE1    CZ   CE2
>    CD2   CE2    CZ   CE1
>    CD1   HD1    CG   CE1
>    CD2   HD2    CG   CE2
>    CE1   HE1   CD1    CZ
>    CE2   HE2   CD2    CZ
>     CZ    HZ   CE1   CE2
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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