Dear Prof. Case and amber users,
I was a bit confused with the usage of -ek flag. So "sqm.in" was written in
the file instead of "tight_p_conv=0"
After giving the following command the calculation has completed
successfully as follows.
Thank you Prof. Case, Jason and Daniel.
Thank you all for your comments and timely suggestions.
------------------
[vaibhav.localhost VD69_repeat]$ antechamber -ek tight_p_conv=0 -i
VD69_2.pdb -fi pdb -o VD69_2.prepin -fo prepi -c bcc -s 2
Running: /opt/amber11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /opt/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 280; net charge: 0
Running: /opt/amber11/bin/sqm -O -i sqm.in -o sqm.out
Running: /opt/amber11/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p /opt/amber11/dat/antechamber/BCCPARM.DAT -s 2
-j 1
Running: /opt/amber11/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i
ANTECHAMBER_AM1BCC_PRE.AC
Running: /opt/amber11/bin/prepgen -i ANTECHAMBER_PREP.AC -f int -o
VD69_2.prepin -rn "UNN" -rf molecule.res
[vaibhav.localhost VD69_repeat]$
On Sun, Aug 28, 2011 at 7:15 PM, case <case.biomaps.rutgers.edu> wrote:
> On Sat, Aug 27, 2011, vaibhav dixit wrote:
>
> > I have made the indicated changes in the sqm.in file (Please check the
> > attached file).
> >
> > Running: /opt/amber11/bin/sqm -O -i sqm.in -o sqm.out
> > Cannot match namelist object name sqm.in
>
> This is a good indication that you input is wrong.
>
> You file was this:
>
>
> Run semi-empirical minimization
> &qmmm
> sqm.in qmcharge=0,
> /
> 6 C1 5.0870 -2.1960 0.7800
> 6 C2 6.4190 -2.1210 0.3500
>
> ....
>
> This is wrong; please see the sqm chapter, and especially note 6 on p. 88,
> for details on the input format. Items in a namelist are in the form
> variable=value, never just an input file name.
>
> I didn't have any problems with your molecule. I've attached the sqm.out
> file (with verbosity set to 1 to see more details).
>
> ...good luck....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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Received on Mon Aug 29 2011 - 10:00:02 PDT
