Message from Junmei Wang below clears up two problems in this thread:
1. The reason acdoctor failed was because the input pdb was not formatted
correctly. (Perhaps acdoctor should have diagnosed this problem as well,
but once things get in the wrong columns in PDB files, it is very difficult
to un-do the damage.)
2. Here is another case where mopac converges, whereas sqm and Gaussian 09
did not. Afficianadoes of sqm convergence problems may want to see if they
can figure out why.
Thanks to Junmei for the help.....dac
----- Forwarded message from Junmei Wang <junmwang.yahoo.com> -----
Date: Thu, 17 Nov 2011 07:46:22 -0800 (PST)
From: Junmei Wang <junmwang.yahoo.com>
I found the lines from "ATOMÂ Â Â 10" to "ATOMÂ Â 38" shift one
column. This is probably the reason leads to acdoctor fail. pdb format is
very tricky and the fields must be reside in certain columns.
>From the graphics, I can see the net charge of this molecule is -1.
I ran the following command to assign am1bcc charges:
antechamber -fi pdb -fo mol2 -i tps.pdb -o tps_am1bcc.mol2 -nc -1 -c bcc
This command failed since sqm cannot converge.
Then I replace sqm with mopac and the command can be run smoothly:
antechamber -fi pdb -fo mol2 -i
tps.pdb -o tps_am1bcc.mol2 -nc -1 -c bcc -df 0
Please find the attached tps_am1bcc.mol2 file
Junmei
----- End forwarded message -----
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Received on Thu Nov 17 2011 - 09:00:03 PST
