Efi Mantzourani wrote:
Ok, tried the specbond. That doesn't work on its own. So I changed the
forcefield N-terminus database (*.tdb) to give me an extra option for
the terminus, [NH]. It seems to work fine, places the hydrogen in the
peptide bond, but doesn't know anything about bond angles and dihedrals
containing the new atom, fair enough. I then went to the *.itp file of
that chain, and filled in the data missing (around 7-8, easy enough).
And it seems to work know!
don't forget the pairs (1-4)
*/David van der Spoel <[EMAIL PROTECTED]>/* έγραψε:
Efi Mantzourani wrote:
> Hi David,
>
> had a look for the specbond entry, but apparently it is for
creating a
> bond between ligand and receptor. I don't have that. Mine is not a
> special bond. it is just that pdb2gmx tries to find a terminus
for all
> the chains.
just try it anyway. you may have to sepcify the specific residue
type of
the N-terminus and C-terminus.
>
> */David van der Spoel /* έγραψε:
>
> Efi Mantzourani wrote:
> > Hi all,
> >
> > I am trying to run a gromacs trajectory on a ligand-receptor
> complex,
> > where the ligand is a head-to-tail cyclic peptide. I add the -ter
> option
> > in the pdb2gmx command, so that i can turn off the charged
> termini in
> > the peptide. Unfortunately, it will only work keeping the N
> terminus as
> > -NH2 (meaning it will add two hydrogens on the resulting
> structure) or
> > as N (in this case it doesn't add any hydrogens). They are both
> wrong,
> > as I want one hydrogen, like in a normal peptide bond. If i try to
> > change the resulting files manually its a pain! The gro file is
easy
> > enough, but the topology file has to be altered so that the added
> > hydrogen is in the correct atom and residue serial number. That
> means i
> > have to change all the remaining atoms, all angles, dihedrals
> etc. Its
> > just impossible as my complex has about 3.000 atoms! Any
> suggestions???
>
> try making a specbond entry, you have to make sure that the
coordinates
> are OK. please report back if succesfull.
> >
> >
>
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>
________________________________________________________________________
> 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
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________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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