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

From: FyD <>
Date: Mon, 16 Mar 2015 13:31:01 +0100

Dear Sohag,

You could use R.E.D. Server Dev./PyRED at:

You can easily run a test providing the PDB input file (with a total
charge = +1 in columns 79/80 of that PDB file for that O+ atom).

You can let PyRED do the job automatically or provide your own options:
   - different theory levels for QM computations
   - provide your own FF parameters using the frcmod.user file
   - provide your own atom types; see MOLECULE1-ATMTYPE

regards, Francois

> 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
> frozen
> 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 - 06:00:04 PDT
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