[AMBER] facing problem to create a prmtop file for oxonium cation

From: Sohag Biswas <cy13p1001.iith.ac.in>
Date: Mon, 16 Mar 2015 15:29:06 +0530

Dear amaber users,

In attempt to create a topology file for oxonium cation from pdb file by
following command, it is showing,

For atom[1]:O1, the best APS is not zero, bonds involved by this atom are

The command line is

antechamber -i eth.pdb -fi pdb -o eth.prepi -fo prepi -c bcc -nc 1 -at gaff
-pf y

It will be very helpful for helping me. Many Many thanks to all. Here i am
attaching also the pdb file which i created by xleap.

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Received on Mon Mar 16 2015 - 03:00:02 PDT
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