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

[David van der Spoel]

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 <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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-- 
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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