Dear Sir,
Thank you for the reply. The entire details are given below.
All the generated files are attached with this mail. There was no other
error message.
So I cannot generate parameter file and topology files using antechamber for
say more than 200 atoms or so, is it?
One thing I noticed is that, ANTECHAMBER_AM1BCC_PRE.AC file has charges for
atoms upto only 164 (my system contains 192 atoms). So I was thinking of
using these intermediate files to obtain .mol2 file. Can that be done?
Hoping for an early reply. Thank you.
with regards,
Chidambar
On Tue, Sep 27, 2011 at 5:23 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Sep 27, 2011, Chidambar Kulkarni wrote:
>
> > I am trying to generate .mol2 file from a
> .pdb
> > file for an organic molecule containing 192 atoms. The sqm seems to run
> > properly but the .mol2 file is not created. The command used to run the
> job
> > is given below.
> >
> > $AMBERHOME/exe/antechamber -i ABC.pdb -fi pdb -o xyz.mol2 -fo mol2 -c bcc
> -s
> > 2
> >
> > >From the sqm.out file it seems that the geometry is converged and the
> > calculation is complete. Can anyone help me to understand what is the
> error
> > and how to overcome it.
>
> No, not without more information that might allow us to reproduce the
> problem. You don't even say whether any other files were created, or
> whether
> there were any other messages. 192 atom is a lot, but probably achievable,
> since you say sqm finished correctly.
>
> ....dac
>
>
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>
--
Chidambar k
Int.PhD
JNCASR
Bangalore
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- application/octet-stream attachment: sqm.in
- application/octet-stream attachment: sqm.out
Received on Tue Sep 27 2011 - 09:30:02 PDT
