Hi Michele,
The amb2gro_top_gro.py script in AMBER may help: you can search the AMBER manual by using the script name for relevant information: https://ambermd.org/doc12/Amber20.pdf <https://ambermd.org/doc12/Amber20.pdf>.
Pengfei
> On Oct 31, 2020, at 5:08 AM, Michele Vanini <michele.vanini.student.kuleuven.be> wrote:
>
> Dear all,
>
>
> I am writing you because i am experiencing some problems using acpype.
>
>
> I followed the Amber tutorial: Setting Up A Polyethylene Terephthalate (PET) Polymer System. (http://ambermd.org/tutorials/advanced/tutorial27/pet.htm)
>
> Everything works.
>
>
> After that i tried to convert the pet20.prmtop<http://ambermd.org/tutorials/advanced/tutorial27/files/pet20.prmtop> and pet20.inpcrd<http://ambermd.org/tutorials/advanced/tutorial27/files/pet20.inpcrd> in Gromacs file using acpype.
>
>
> acpype.py -p pet20.prmtop -x pet20.inpcrd
>
>
> The files .top and .gro were correctly generated. The problem is that running a simple energy minimization on Gromacs with a single component in vacuum there is something wrong: the structure is like dissembled.
>
> On my opinion, there is something wrong during the conversion from Amber to Gromacs, maybe in the topology file.
>
>
> Do you have any suggestion?? Have you ever come across similar issues?
>
>
> Best regards,
>
> Michele Vanini
>
>
>
>
>
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Received on Fri Nov 20 2020 - 09:00:02 PST
