[AMBER] RES: error_antechamber (QMMM: ERROR!)

From: <gustavo.seabra.gmail.com>
Date: Fri, 3 Aug 2018 15:56:45 -0300

Hi Atila,

I don´t know what is going wrong with your installation. I tried both, and
they worked just fine for me here. The commands I used were:

$ $AMBERHOME/bin/antechamber -i imt.pdb -fi pdb -o imt.mol2 -fo mol2 -c bcc
-s 2
$ $AMBERHOME/bin/antechamber -i srf.pdb -fi pdb -o srf.mol2 -fo mol2 -c bcc
-s 2

And here are the mol2 files created:

https://www.dropbox.com/s/km0wb65tbs0fulj/imt.mol2?dl=0
https://www.dropbox.com/s/irwfoz7nk7f16ej/srf.mol2?dl=0

(I only changed the ligand name in the file, for cosmetic purposes, *after*
running Antechamber.)

I suggest you try running the test cases there to check your install.

All the best,

--
Prof. Gustavo Seabra
Chemistry Department
Federal University of Pernambuco, Brasil
.gmseabra
-----Mensagem original-----
De: Atila Petrosian <atila.petrosian.gmail.com> 
Enviada em: sexta-feira, 3 de agosto de 2018 12:52
Para: amber <amber.ambermd.org>
Assunto: [AMBER] error_antechamber (QMMM: ERROR!)
Dear Gustavo,
Thanks for your answer.
I have 2 ligands. I got them from pubchem database.
I optimized one of them using gaussian software. But both of them have same
error when using antechamber.
imt.pdb  (with energy optimization)
https://1drv.ms/f/s!AveJH4Y30cH0rEU08meMh0EEfQde
srf.pdb (without energy optimization)
https://1drv.ms/u/s!AveJH4Y30cH0sQxETzLmmhHJIY8G
How to resolve it?
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Received on Fri Aug 03 2018 - 12:00:02 PDT