Θέμα: Re: Θέμα: Re: [gmx-users] cyclic peptides

[Efi Mantzourani]

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!

David van der Spoel <spoel at xray.bmc.uu.se> 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.
>     ________________________________________________________________________
>     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://folding.bmc.uu.se
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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://folding.bmc.uu.se
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