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:
>
> 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
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?
....regards...dac
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
