Re: [AMBER] Problem in creating .mol2 and .frcmod files

From: David A Case <>
Date: Wed, 9 Oct 2013 10:22:02 -0400

On Wed, Oct 09, 2013, Vijayalaxmi Sahoo wrote:

> I am currently working in centos release 6.4. I tried creating .mol2 and
> .frcmod files for bmim molecule from the commands given in the antechamber
> 1.27( AMBER tutorials). The link for the AMBER tutorial is provide below:
> I used the same commands given in the tutorials on the same input files
> given there but the results are not at all matching. The charges for .mol2
> file i got are different from those in tutorials and for .frcmod file the
> number of improper are different.
> The command used for .mol2 file:
> antechamber -i bmim.pdb -fi pdb -o bmim.mol2 -fo mol2 -c bcc -nc 1
> For .frcmod file:
> parmchk -i bmim.mol2 -f mol2 -o frcmod.bmim

Works for me: that is, starting from your PDB file, I get mol2 and frcmod
files that are the same as in the tutorial, and are different from the
ones you are getting.

What version of AmberTools are you using?


p.s.: please avoid duplicate postings. Volunteers try to answer questions
as quickly as they can.

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Received on Wed Oct 09 2013 - 07:30:05 PDT
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