Dear Prof. Case and Amber users,
I have made the indicated changes in the sqm.in file (Please check the
attached file).
I have used the optimized geometry of VD69 at am1 level using gaussian03.
Also I have incorporated the -ek flag, but the error is persistent.
Please suggest on what changes do I need to make in the sqm.in file and
whether the am1 optimized geometry is good enough?
Thank you.
[vaibhav.localhost VD69]$ antechamber -ek sqm.in -i VD69_am1opt.pdb -fi pdb
-o VD69_2.prep -fo prepi -c bcc 2
Total number of electrons: 280; net charge: 0
Running: /opt/amber11/bin/sqm -O -i sqm.in -o sqm.out
Cannot match namelist object name sqm.in
[vaibhav.localhost VD69]$
On Fri, Aug 26, 2011 at 6:05 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Fri, Aug 26, 2011, vaibhav dixit wrote:
>
> > I have used the following command in amber11 i.e. am1bcc in amber11 and
> bcc
> > in amber10.
> > But command with bcc is not successful due to convergence failure in
> > amber11.
>
> > [vaibhav.localhost VD69]$ antechamber -i VD69.pdb -fi pdb -o VD69_1.prep
> -fo
> > prepi -c am1bcc -s 2
>
> OK...what is happening is that antechamber doesn't recognize the "am1bcc"
> flag, but doesn't give any error message. Hence, it doesn't calculate any
> charges (all the charges in your prep file are zero). So, the program
> finishes, but it doesn't "work" in any real sense.
>
> (Volunteers are hereby solicited to get antechamber to emit appropriate
> messages when it finds command line arguments it doesn't recognize.)
>
> I don't know if you ever posted the VD69.pdb file that causes the problem
> with
> sqm. It is sometimes that case that starting with a better initial
> geometry
> (e.g. by minimizing in some other program like Gaussian) allows sqm to
> work.
> But the more examples we have of lack of convergence in sqm, the more
> likely
> it is that we can figure out what do to.
>
> ....dac
>
>
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>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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- application/octet-stream attachment: sqm.in
Received on Fri Aug 26 2011 - 23:00:02 PDT
