[AMBER] How to computing peptide partial charges with antechamber?

From: <yulongsun.nwpu.edu.cn>
Date: Sat, 29 Sep 2018 21:59:53 +0800

Hi Ambers,
Would you please tell me how to use antechamber to calculate the charge of peptide?
I noticed that there are tutorial for computing compound’s charge with cmd:
 
antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2
http://ambermd.org/tutorials/basic/tutorial4b/
 
or tell me to download the .cif file from rcsb. However, my protein is homology-modelled….
http://ambermd.org/tutorials/basic/tutorial5/
 
but it did not work for peptide…

Yulong



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Received on Sat Sep 29 2018 - 07:00:02 PDT