U must first install ambertools (its fortunately free!). Then make your .prmtop and .crd files using tleap or xleap (included in Ambertools). then use this file to convert .prmtop and .crd files to .top and .gro files

https://www.dropbox.com/s/rfjpz45we1f5h0z/amb2gmx_dihe_old.pl

Yes, you can make GROMACS topology file.

A python script will do that: http://code.google.com/p/acpype/

U must first install ambertools (its fortunately free!). Then make your .prmtop and .crd files using tleap or xleap (included in Ambertools). then use this file to convert .prmtop and .crd files to .top and .gro files

https://www.dropbox.com/s/rfjpz45we1f5h0z/amb2gmx_dihe_old.pl

How valid is this conversion?

Hi,

Is parmed.py (which will come along with AMBER Tools)  will do the same ? if Yes , can anyone please explain how to use this script to convert AMBER topology to gromacs toplogy ?

Thanks in advance.

Anji Babu

hello, Amir are you sure tleap and xleap if free in AMbertools? if yes can you please suggests how to make .prmtop files?

Because my ACPYPE server is failed due to unavailability of .prmtop files

Hi Sourav

You can use a python script in amber tools to convert them you have to introduce

Parmed , write a script in python like underneath say scritpt.py

"import parmed as pmd

parm = pmd.load_file('sustiva.prmtop' ,'sustiva.inpcrd')

parm.save('lig.itp',format='gromacs')

parm.save('lig.gro')

(NB: sustiva is just used as an example)

and then use

amber.python script.py

Xleap and Tleap is free as they come in AmberTools and don't forget to install Python while you try and install AmberTools.

Best Of luck