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

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Wed Aug 22 09:05:14 CEST 2007


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.



 Florian Haberl                        
 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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