Subject: Re: CCL: Not really a summary "Free softw. for pot. energy calc."

From: Francois Sampieri <[email-masked]>
Date: Tue, 15 Jan 2002 16:02:25 +0200

Dear all,

Almost one week ago, I sent a message to the list for getting help in a
batch calculation of potential energy of many protein structures. I'm
wondering if my question was well formulated since I obtained only one
response (Thanks again Marc!) as a proposal for compiling for me the (few)
softwares I had yet got as source code only.
Unfortunately, I soon realized that the executables that Marc sent to me
will not solve my present problem, though these softwares could be very
useful in other respects.
I would like to understand such a poor response, and I wonder if I
under-estimated the complexity of the process of potential energy
calculations. These must be performed with sophisticated force field
algorithms and generally, such FF are part of packages which are rarely
free.
So, I resign myself to cope with what I'm equipped with:  INSIGHT II or
MODELLER, even if they are not the best solution for the type of
calculation I want to perform.
I will inform the list if I eventually succeed.
Best regards

Francois Sampieri

___________________
My previous message:

>
>I have to sort a huge number (more than 3000 pdb files) of conformations of
>the same protein, according to their potential energies (bonded +
>non-bonded).
>The first step could be to automatically launch a software capable of
>achieving energy calculation from each pdb file, then to extract the energy
>values from the ca. 3000 created files, and sort them into a single file,
>the all processes being driven by a Perl script running on O2 SGI under
>Irix 6.5.
>I got references for some such free softwares, but I found them as source
>files only and this is a problem for us since we don't have (and don't have
>skills for coping with) Fortran or C compilers.
>
>After unsuccessfully searching on the Web, I'm asking to the CCL community
>if anyone could point me to such executable programs.
>All responses will be summarized.
>

____________________________________________
UMR 6560 CNRS-Universite de la  Mediterranee
Laboratoire de Biochimie - IFR Jean Roche
Faculte de Medecine Nord
Bd Pierre Dramard
13916 Marseille Cedex 20
E-mail: [email-masked]
Fax: (33) 4 91 65 75 95
Tel: (33) 4 91 69 88 44

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From: "CUI, Guanglei" <[email-masked]>
Date: Tue, 15 Jan 2002 11:20:14 -0500 (EST)

Hi, 
    You happen to have AMBER6. The sander module can post-process a trajectory
file and calculate the potential energy of each structure it has with imin = 5.
It might not be the best solution for you but at least it could be a try. Good 
luck.

Guangelei Cui

On Tue, 15 Jan 2002, Francois Sampieri wrote:

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-- 
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790

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From: "CUI, Guanglei" <[email-masked]>
Date: Tue, 15 Jan 2002 13:18:44 -0500 (EST)

It's going to be in AMBER7. Sorry about the confusion. 

Regards,

-- 
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790