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(unknown)


Hi again, Charles

Actually, in my previous e-mail (testDist) the version used was 2.9.3 and not
1.9.3. A typo, sorry about that.

Downloaded the new 2.9.4 version. Untaring the two packs it gives me only one
directory. Configure went without errors in a ia32 linux box. Tryed the
testDist, and all went smoothly. No errors. Just one question. When I type
xplor in my console, it says the following:

Could not find platform independent libraries <prefix>
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
                       XPLOR-NIH version 2.9.4
..

Do not understand why it gives me such error.

Another question, this time in a SGI Octane R10000, running 6.5.11.
When performing the ./configure, it gives me the following error:

R O O T:zeus 21# ./configure
37105:/octa1/software/xplor-nih-2.9.4/bin.IRIX64_6.5/xplor: rld: Fatal Error:
attempted access to unresolvable symbol in
/octa1/software/xplor-nih-2.9.4/bin.IRIX64_6.5/libpy.so: _xpg5_vsnprintf

Any help is appreciated.

Best regards,
(Continue reading)

Tomasz Cierpicki | 12 Mar 21:45 2004

%POWELL-ERR

Hi

I have some problems to generate correct structure files in xplor-nih.
Minimization of original pdb file stops with very high bond/angle/improper
energies and error message:

 --------------- cycle=    35 ------ stepsize=    0.0000 --------------
| Etotal =2675.554 grad(E)=17.466   E(BOND)=175.944 E(ANGL)=863.045 |
| E(DIHE)=0.000    E(IMPR)=1998.340 E(VDW )=-150.215 E(ELEC)=-211.560 |
-----------------------------------------------------------------------
 %POWELL-ERR: Line search abandoned

There is no such problem generating structure file from the sequence.
Does anyone know what is the problem?

Thanks
Tomasz Cierpicki

John Kuszewski | 12 Mar 22:33 2004
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Re: %POWELL-ERR

Tomasz Cierpicki wrote:
> 
> Hi
> 
> I have some problems to generate correct structure files in xplor-nih.

It's not clear to me what you're trying to do here.  Are you trying to
get
initial coordinates to start a structure determination?  Are you trying
to 
refine a known structure, starting from its PDB entry's coordinates?  

I'm going to assume that you mean that you've created a PSF file from
the 
sequence, and now need to get some starting coordinates with good
covalent 
geometry.  

> Minimization of original pdb file stops with very high bond/angle/improper
> energies and error message:
> 
>  --------------- cycle=    35 ------ stepsize=    0.0000 --------------
> | Etotal =2675.554 grad(E)=17.466   E(BOND)=175.944 E(ANGL)=863.045 |
> | E(DIHE)=0.000    E(IMPR)=1998.340 E(VDW )=-150.215 E(ELEC)=-211.560 |
> -----------------------------------------------------------------------
>  %POWELL-ERR: Line search abandoned

There are two problems with what you seem to be doing.  First, it
appears
that you forgot to issue a flags statement before starting the
(Continue reading)

Nuno R. L. Ferreira | 16 Mar 17:06 2004
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TADBP vs solvent

Hi *

I am calculating a nmr structure of a peptide in methanol.
>From what I read, this database comes from crystal structures.
So, can I apply these a priori restraints? Or this approach is only valid for 
aqueous solution nmr structures determinations?

Best regards,
Nuno

------------------------------------
Departamento QuĂ­mica
Universidade Coimbra
Portugal

www.biolchem.qui.uc.pt
------------------------------------

John Kuszewski | 16 Mar 17:23 2004
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Re: TADBP vs solvent

"Nuno R. L. Ferreira" wrote:
> 
> I am calculating a nmr structure of a peptide in methanol.
> From what I read, this database comes from crystal structures.
> So, can I apply these a priori restraints? Or is this approach only valid for
> aqueous solution nmr structures determinations?

For peptides, it is probably reasonable to use the DELPHIC torsion
potential 
for structures calculated in non-aqueous solvents.  This is because 
the locations of populatable regions of torsion angle space, and their 
relative populations, are almost entirely determined by excluded volume
effects, which obviously don't depend on the solvent.

However, it is probably not reasonable to use the DELPHIC torsion 
potential to calculate nucleic acid structures in non-aqueous
environments.
Nucleic acids have far more degrees of freedom along their backbones 
than peptides, and their populated regions are determined far more by 
electrostatic effects, which will obviously change with the solvent.

--John Kuszewski

--

-- 
Dr John Kuszewski

301-594-5831 (voice)
301-402-2867 (fax)
John.Kuszewski <at> nih.gov

(Continue reading)

Nuno R. L. Ferreira | 16 Mar 17:45 2004
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Re: TADBP vs solvent

Ups.  Think I sent an email to your personal account, Dr. Kuszewski.
Just to stay in the mailing list thread, I'm sending again the "same" message 
to the list.

>
> For peptides, it is probably reasonable to use the DELPHIC torsion
> potential
> for structures calculated in non-aqueous solvents.  This is because
> the locations of populatable regions of torsion angle space, and their
> relative populations, are almost entirely determined by excluded volume
> effects, which obviously don't depend on the solvent.
>
Thanks.
This DELPHIC torsion potential is implemented in files under 
/databases/torsions_raw ?

Nuno

Cinque Soto | 16 Mar 23:08 2004

XPLOR-NIH modifications

Where might we find information on using the GB module developed 
by Tom Simonson?

-Cinque Soto

Charles | 17 Mar 00:26 2004

Re: XPLOR-NIH modifications


Hi Cinque--

> Where might we find information on using the GB module developed 
> by Tom Simonson?

a very simple example can be found in test/gborn.inp
All of the required parameters (i.e. Amber) should be present in the
Xplor-NIH distribution. Please let me know if this is not the case.

More info can be found in the appropriate references. e.g.
T Simonson, Curr Opin Struc Biol, 2001, 11:243
you might also contact Tom directly.

regards--
Charles
Nuno R. L. Ferreira | 19 Mar 23:24 2004
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itype=powell,pc6

Hi all

I read some of the inp scripts on the ginputs folder, trying to understand the 
meaning of the several flags inside de dynamics internal statement. Some of 
them I really do not know its purpose.
Is this information somewhere else?

Best regards,
Nuno

Charles | 19 Mar 23:39 2004

Re: itype=powell,pc6


Hi--

>  I read some of the inp scripts on the ginputs folder, trying to
> understand the meaning of the several flags inside de dynamics
> internal statement. Some of them I really do not know its purpose.
> Is this information somewhere else?

there are a few sources of help:

1) online help:
  % xplor
  X-PLOR>dynamics internal
  Internal Dynamics>help

2) the IVM paper:
  Schwieters, C.D. & Clore, G.M. (2001) Internal coordinates for
   molecular dynamics and minimization in structure determination and
   refinement. J. Magn. Reson. 152, 288-302.

3) the help pages for the python IVM interface:
  in helplib/nih-py-ivm

for the query in the subject string:
``powell'' directs the ivm to perform powell minimization
``pc6''    directs the ivm to perform dynamics (using the pc6 integrator)

regards--
Charles
(Continue reading)


Gmane