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 Sat Oct 31 2020 - 02:30:02 PDT
