RE: Can paratools really parametrize a structure? Is it really finished?

From: JC Gumbart (
Date: Mon Feb 28 2011 - 11:23:54 CST

It is not complete, but hasn't been under active development in years. Any
use of it should therefore be considered experimental.


That being said, I just tried the following steps in Paratool without any


1) Load parent molecule (***pdb)

2) Load base molecule (***pdb)

3) import optimized geometry (A.log)

4) import hessian/charges from SP calc (B.log)


If those same steps in a fresh VMD don't work, it's possible something with
your log file is causing issues.



From: [] On Behalf
Of Ranyere Deyler
Sent: Monday, February 28, 2011 10:57 AM
Subject: namd-l: Can paratools really parametrize a structure? Is it really


Dear VMD/NAMD users. I've searched on the mail list and i've found two
peopple with the same problem, but the other times no one answeared. And
looking at thousand of others problems, i ask myself if anyone has ever
managed to parametrize a structure using para tools. I wanted to know if
it's really possible to use it for parametrize, because if not, i'll just
stop trying.


Here goes my problem again, let's try for the last time.

What happens is that i run on Gaussian the Hessian/Charges "Single Point
calculation". Then i get the log file and load it on paratool. But when i do
that, comes the errors:

"couldn`t read internal coordinate table'' and

"could not load pdb file TEST_FINAL.log"

Lot's of peopple had the same problem, without solution, and i think they've
just given up.

It loads correctly the first file, the "gaussian geometry optimization" ,
but the second one, the Hessian/charges single point calculation it never
So, i'm stuck here, i'm not the first one the present this problem that
until now it has not been solved.

Does anyone knows how to fix this? I don't know what to do, tryed
everything, but it never loads the Hessian file.

Thanks everyone.

Ranyere Deyler Trindade

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