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

From: Vijayalaxmi Sahoo <vlsahoo.rgp.gmail.com>
Date: Wed, 9 Oct 2013 19:08:28 +0530

Hello people,

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:

 http://ambermd.org/tutorials/advanced/tutorial15/Tutorial2.xhtml

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

The input files that i have used are attached below:

Kindly tell me how to overcome this problem.

Thanks.
Vijayalaxmi Sahoo


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Received on Wed Oct 09 2013 - 07:00:04 PDT
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