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

From: Ranyere Deyler (ranyere_at_gmail.com)
Date: Mon Feb 28 2011 - 13:28:30 CST

It's on the "4th" step that it doesn't work. I get the log from the SP on
Gaussian, but when i try to load on paratool it returns the error that i
showed
on last email. Wich version of Gaussian did you use? Because Axel sayd that
the outputs of gaussian may change, I'm using the gaussian 03.
The optmized geometry is loaded without any error. Only the SP cal. I'm
about to give up on gaussian.

Thanks a lot!

On Mon, Feb 28, 2011 at 2:23 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:

> It is not complete, but hasnít 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
> issues:
>
>
>
> 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 donít work, itís possible something with
> your log file is causing issues.
>
>
>
>
>
> *From:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *On
> Behalf Of *Ranyere Deyler
> *Sent:* Monday, February 28, 2011 10:57 AM
> *To:* namd-l_at_ks.uiuc.edu
> *Subject:* namd-l: Can paratools really parametrize a structure? Is it
> really finished?
>
>
>
> 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
> loads.
> 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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