Subject: error in orthogonality

From: Demetrios Xenides <qc2<<at>>chemistry.upatras.gr>
Date: Fri, 02 Jul 2004 12:14:19 +0200

Hi all!!!
Gaussian plays tricks again. The same file in G94 runs without any 
problem but in G98 it reduces the number of the basis used... I am 
trying to run a single point calculation using an uncontracted basis set 
by partridge.

same command line for both
#p rhf/gen scf(conver=10) nosymm field=read

-------------------------------------------- MESSAGE IN 
------------------------------------
---------------------------------------------------G98--------------------------------------------
Two-electron integral symmetry is turned off.
   187 basis functions      196 primitive gaussians
    26 alpha electrons       26 beta electrons
       nuclear repulsion energy       147.4020983233 Hartrees.
 Leave Link  301 at Fri Jul  2 09:46:53 2004, MaxMem=    6291456 
cpu:       0.1
(Enter /usr/local/g98/l302.exe)
 One-electron integrals computed using PRISM.
 Error in orthogonal basis= 1.61D-07 with   187 functions, increasing 
threshold to 2.00D-04.
 Error in orthogonal basis= 1.61D-07 with   187 functions, increasing 
threshold to 4.00D-04.
 Error in orthogonal basis= 1.61D-07 with   187 functions, increasing 
threshold to 8.00D-04.
 Error in orthogonal basis= 1.61D-07 with   187 functions, increasing 
threshold to 1.60D-03.
 Error in orthogonal basis= 1.61D-07 with   187 functions, increasing 
threshold to 3.20D-03.
 Error in orthogonal basis= 1.61D-07 with   187 functions, increasing 
threshold to 6.40D-03.
 Error in orthogonal basis= 1.61D-07 with   187 functions, increasing 
threshold to 1.28D-02.
 Error in orthogonal basis= 1.61D-07 with   187 functions, increasing 
threshold to 2.56D-02.
 Error in orthogonal basis= 4.12D-08 with   186 functions, increasing 
threshold to 5.12D-02.
 Error in orthogonal basis= 3.10D-09 with   182 functions, increasing 
threshold to 1.02D-01.
 NBasis=   187 RedAO= T  NBF=   187
 NBsUse=   167 1.02D-01 NBFU=   167

-------------------------------------------- MESSAGE IN 
------------------------------------
---------------------------------------------------G94W------------------------------------------

Two-electron integral symmetry is turned off.
   187 basis functions      187 primitive gaussians
    26 alpha electrons       26 beta electrons
       nuclear repulsion energy       147.4020983233 Hartrees.
 Leave Link  301 at Fri Jul 02 10:22:17 2004, MaxMem=    4000000 cpu:1.0
 (Enter C:\G94W\l302.exe)
 One-electron integrals computed using PRISM.
 The smallest eigenvalue of the overlap matrix is  2.425E-04
 Leave Link  302 at Fri Jul 02 10:22:17 2004, MaxMem=    4000000 cpu:1.0
 (Enter C:\G94W\l303.exe)

any hint?

Cheers
Demetrios

---

From: Eric Bennett <ericb<<at>>pobox.com>
Date: Fri, 02 Jul 2004 11:09:12 -0500

Michel Petitjean wrote:

>To: chemistry<<at>>ccl.net
>Subject: CCL:software to convert  XYZ format to PDB ?
>
>Konrad Hinsen <hinsen<<at>>cnrs-orleans.fr> wrote:
>  
>
>> If I had to do this (fortunately I don't), I'd first identify the
>>
>>peptide planes as patterns of pairwise distances (they are quite 
>>rigid). I'd then identify the sidechains atom by atom starting from the 
>>C-alphas, again by distance criteria. Not a trivial task, but not an 
>>impossible one either.
>>    
>>
>
>Sure... if you have the side chains ! (were not indicated in the example)
>It needs other assumptions: true residues, no HETATM, lexicographical
>ordering coherent with the PDB conventions...
>  
>
There are programs (such as ARP/wARP) which start with NO atom information, not even coordinates, and can correctly build a protein structure based on an electron density map using pattern recognition techniques.  The ambiguities there, such as ASP vs. ASN, are not present when you know the elements, as we do here.  ARP/wARP is also gaining ligand building capabilities and already handles water molecules.

ARP is part of CCP4 so you get source code with it.
http://www.embl-hamburg.de/ARP/

Of course if you have any unexplained data (whether electron density or known atom positions) that do not fit the pattern of an amino acid, you can just leave them alone and inform the user.

-- 
Eric Bennett, Center for Drug Design, U of Minnesota