[gmx-users] multichain peptide simulation

[David van der Spoel]

On Wed, 2004-05-05 at 12:18, Susan Idiula wrote:
> Hi,
> 
> I am simulating six heptapeptides (as different chains) in water. Each
> peptide has the N terminus as -CO-CH3 and the C-terminus as NH-CH3.The
> simulation works well but when I use xrama and g_rama to check dihedral
> angles. I get the following error:
> 
> Fatal error: Dihedral X, Y not found in topology. (X,Y are the atom
> numbers of O of -CO of 7th residue and Y is the atom number of H of NAC as
> mentioned in the .top file created by pdb2gmx)

it seems like g_rama is misinterpreting the protein as being a single
chain. maybe you can use an index file.

> 
> Everything works nicely with one heptapeptide.
> 
> These are the topology of the extra groups that I have introduced in the
> ffG43a1.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
>    CA     C     O    ga_29
>  [ impropers ]
>     C    CA    +N     O    gi_1
>  [ dihedrals ]
>    CA  C  +N  +CA  gd_4
> 
> [ NAC ]
>  [ atoms ]
>     N   N   -0.280  0
>     H   H    0.280  0
>     CA  CH3  0.000  1
>  [ bonds ]
>     N   H    gb_2
>     N   CA   gb_20
>  [ angles ]
>    -C   N   H   ga_31
>     H   N   CA  ga_17
>    -C   N   CA  ga_21
>  [ impropers ]
>     N  -C   CA   H   gi_1
>  [ dihedrals ]
>     -CA -C  N  CA  gd_4
> 
> I have 7 residues per chain, so in principle I should be getting 7x6 =42
> phi-psi combinations, but xrama calculates 47 phi-psi combinations. i
> presume it has to do something with the ends of each chain, but i am not
> sure.
> 
> i have tried removing the extra CO-CH3 AND NH-CH3, but it didnot work.
> 
> any suggestions?
> 
> 
> thanx
> susan
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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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