[gmx-users] multichain peptide simulation

[David van der Spoel]

On Fri, 2004-05-07 at 04:52, Susan Idiula wrote:
> Hi,
> 
> I tried using an index file. it does not seem to work. is there any other
> alternative?
a bit laborious, but you can split the trajectory using trjconv and the
index file in one traj for each protein (and you will have to make a
special tpr for that as well).
> 
> thanks
> susan
> 
> 
> > 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%2
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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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