[gmx-users] Can I convert Amber (.prepin) into Gromacs (.itp) topology?

[SeungPyo Hong]

Thank you very much Florian!
It is what I want to know and I can successfully transform from amber format
to gromacs format!

Sincerely,
Seungpyo Hong

On 8/22/07, Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de> wrote:
>
> Hi,
>
> On Tuesday, 21. August 2007 22:14, SeungPyo Hong wrote:
> > Dear gmx-user,
> > Until yesterday, I believe in PRODRG server.
> > But when I inspect the result carefully, I found it does not make sense
> at
> > all!
> > Of course, its because I did not modify the input and just thought all
> the
> > process will be done automatically.
> >
> > Anyhow, I also found that partial charge is not plausible even after I
> get
> > the plausible structure by adding some options in it.
> > So, I tried amber's antechamber, and get .prepin file and the partial
> > charge in it seems to be reasonable.
> >
> > Then, I want to convert .prepin file into .itp file.
> > Is there a software doing that work?
>
> take a look at http://wiki.gromacs.org/index.php/AMBER
>
> You need to start tleap or xleap to generate top and crd files of your
> molecule, than use the perl skript (amb2gmx.pl) to transfer it to .gro
> and .top file with gromacs format.
> You also need to take the correct forcefield of AMBER.
>
>
> >
> > Or, is gromacs has tool that generate topology parameters like
> antechamber
> > in amber?
> >
> > Thank you for reading.
>
>
> Greetings,
>
> Florian
>
> --
>
> -------------------------------------------------------------------------------
> Florian Haberl
> Computer-Chemie-Centrum
> Universitaet Erlangen/ Nuernberg
> Naegelsbachstr 25
> D-91052 Erlangen
> Telephone:     +49(0) − 9131 − 85 26581
> Mailto: florian.haberl AT chemie.uni-erlangen.de
>
> -------------------------------------------------------------------------------
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-- 
--------------------------------------------------
'God used beautiful mathematics in creating the world.'
-Paul Dirac
'But he created too many objects.'
-Seungpyo Hong

Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
sphong_ at kaist.ac.kr
sp1020 at gmail.com
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