Re: [Rdkit-discuss] SD file read error

[Steve O'Hagan]

OK, error messages where hidden by IPython for me too.

I used "Knime" to look at the sdf file, and it seems that the errors are 
"real" - polymers, organometallic compounds or completely daft, two 
examples:




The structure in the first column is the input sdf.

Simple workflow was:


"RDKit From Molecule" generated exactly the same 36 "broken" molecules 
as the Python script.


There's also one bad sdf record in the file.

Cheers,
Steve.


On 11/01/2017 20:17, Curt Fischer wrote:

I also got this to run with no problem in a Jupyter notebook.

BUT...I did see the error messages Milinda mentioned in the terminal 
that was running the jupyter notebook server.  If I do *from 
rdkit.Chem.Draw import IPythonConsole *before running the code, I see 
all the errors/warnings in Jupyter.


I think this version of the loop is a bit more informative (best to do 
with IPythonConsole disabled):


*from rdkit import Chem
**from rdkit.Chem import Descriptors**
**input_file = 'structures.sdf'**
**suppl  = Chem.SDMolSupplier(input_file)**
**low_mass=50
**high_mass=1000**
**ms = []**
**for idx, mol in enumerate(suppl) :
**  if mol is None:
**  print "No molecule: " + str(idx)
**  continue
**  try:
**  if (mol and
**  round(Descriptors.ExactMolWt(mol), 4) >= low_mass and
**  round(Descriptors.ExactMolWt(mol), 4) <= high_mass
** ):
**
**  ms.append(mol)
**  except:
**  print "Error: " + str(idx)
**  pass*



It shows that all the problems are from rdkit failing to generate 
molecules, i.e. the try/except isn't doing anything.  (Note it is bad 
practice to have a naked *except*).


The first molecule that fails is #491, heparin sulfate. The molecule 
can be imported using *Chem.MolFromInchi()*. This gels nicely with the 
rdkit error message for this molecule:


RDKit ERROR: [12:12:56] Unhandled CTAB feature: S group SRU on
line: 75. Molecule skipped.



The problem is thus the line M STY 1 1 SRU in the mol block, which you 
can see if you do


*suppl.reset() for idx, mol in enumerate(suppl): if idx == 491:
print suppl.GetItemText(idx)*


I don't know enough to pinpoint the precise reason for the error.  And 
there are lots more errors to go through to get everything from HMDB 
into RDKit, it seeems.


Curt

On Wed, Jan 11, 2017 at 11:39 AM, Steve O'Hagan 
> wrote:


With same code and fresh file download, works fine for me without
error.

ms contains 35177 molecules. Perhaps your download was corrupt?


On 11/01/2017 18:26, Milinda Samaraweera wrote:

Dear Experts,

I was trying to read in the attached SD file (downloaded from
HMDB) and trying to calculate the exact mass of each entry:
​
structures.sdf


​
from rdkit import Chem
from rdkit.Chem import Descriptors

suppl  = Chem.SDMolSupplier(input_file)

low_mass=50
high_mass=1000

ms = []

for mol in suppl :

if mol is None: continue

try:
if mol and
round(Descriptors.ExactMolWt(mol),4)>=low_mass and   
round(Descriptors.ExactMolWt(mol),4)<=high_mass:

ms.append(mol)

except:
  pass

By running the script, I got a barrage of errors as:

[13:15:14] ERROR: Could not sanitize molecule ending on line 1993855
[13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater
than permitted
[13:15:14] Explicit valence for atom # 9 O, 3, is greater than
permitted
[13:15:14] ERROR: Could not sanitize molecule ending on line 1994014
[13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater
than permitted
[13:15:14] Explicit valence for atom # 9 O, 3, is greater than
permitted
[13:15:14] ERROR: Could not sanitize molecule ending on line 1996036
[13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater
than permitted
[13:15:16] Explicit valence for atom # 46 N, 4, is greater than
permitted
[13:15:16] ERROR: Could not sanitize molecule ending on line 2302532
[13:15:16] ERROR: Explicit valence for atom # 46 N, 4, is greater
than permitte
[13:15:16] Explicit valence for atom # 16 N, 4, is greater than
permitted
[13:15:16] ERROR: Could not sanitize molecule ending on line 2302918
[13:15:16] ERROR: Explicit valence for atom # 16 N, 4, is greater
than permitte
[13:15:17] Explicit valence for atom # 11 N, 4, is greater than
permitted
[13:15:17] ERROR: Could not sanitize molecule ending on line 2556541
[13:15:17] ERROR: Explicit valence for atom # 11 N, 4, is greater
than permitte
[13:15:18]  S group SUP ignored on line 2836416
[13:15:18] Explicit valence for atom # 1 Cl, 4, is 

Re: [Rdkit-discuss] SD file read error

[Curt Fischer]

I also got this to run with no problem in a Jupyter notebook.

BUT...I did see the error messages Milinda mentioned in the terminal that
was running the jupyter notebook server.  If I do *from rdkit.Chem.Draw
import IPythonConsole *before running the code, I see all the
errors/warnings in Jupyter.

I think this version of the loop is a bit more informative (best to do with
IPythonConsole disabled):


> *from rdkit import Chem**from rdkit.Chem import Descriptors*
> *input_file = 'structures.sdf'*
> *suppl  = Chem.SDMolSupplier(input_file)*
>
> *low_mass=50**high_mass=1000*
> *ms = []*
>
> *for idx, mol in enumerate(suppl) :*
> *if mol is None: *
> *print "No molecule: " + str(idx)*
> *continue*
> *try:*
> *if (mol and *
> *round(Descriptors.ExactMolWt(mol), 4) >= low_mass
> and *
> *round(Descriptors.ExactMolWt(mol), 4) <= high_mass*
> *   ):*
>
> *ms.append(mol)*
> *except:*
> *print "Error: " + str(idx)**pass*



It shows that all the problems are from rdkit failing to generate
molecules, i.e. the try/except isn't doing anything.  (Note it is bad
practice to have a naked *except*).

The first molecule that fails is #491, heparin sulfate.  The molecule can
be imported using *Chem.MolFromInchi()*. This gels nicely with the rdkit
error message for this molecule:

RDKit ERROR: [12:12:56] Unhandled CTAB feature: S group SRU on line: 75.
Molecule skipped.



The problem is thus the line M STY 1 1 SRU in the mol block, which you can
see if you do

*suppl.reset() for idx, mol in enumerate(suppl): if idx == 491: print
> suppl.GetItemText(idx)*
>

I don't know enough to pinpoint the precise reason for the error.  And
there are lots more errors to go through to get everything from HMDB into
RDKit, it seeems.

Curt

On Wed, Jan 11, 2017 at 11:39 AM, Steve O'Hagan 
wrote:

> With same code and fresh file download, works fine for me without error.
>
> ms contains 35177 molecules. Perhaps your download was corrupt?
>
>
> On 11/01/2017 18:26, Milinda Samaraweera wrote:
>
> Dear Experts,
>
> I was trying to read in the attached SD file (downloaded from HMDB) and
> trying to calculate the exact mass of each entry:
> ​
>  structures.sdf
> 
> ​
> from rdkit import Chem
> from rdkit.Chem import Descriptors
>
> suppl  = Chem.SDMolSupplier(input_file)
>
> low_mass=50
> high_mass=1000
>
> ms = []
>
> for mol in suppl :
>
> if mol is None: continue
>
> try:
> if mol and round(Descriptors.ExactMolWt(mol),4)>=low_mass
> andround(Descriptors.ExactMolWt(mol),4)<=high_mass:
> ms.append(mol)
>
> except:
>   pass
>
> By running the script, I got a barrage of errors as:
>
> [13:15:14] ERROR: Could not sanitize molecule ending on line 1993855
> [13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than
> permitted
> [13:15:14] Explicit valence for atom # 9 O, 3, is greater than permitted
> [13:15:14] ERROR: Could not sanitize molecule ending on line 1994014
> [13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than
> permitted
> [13:15:14] Explicit valence for atom # 9 O, 3, is greater than permitted
> [13:15:14] ERROR: Could not sanitize molecule ending on line 1996036
> [13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than
> permitted
> [13:15:16] Explicit valence for atom # 46 N, 4, is greater than permitted
> [13:15:16] ERROR: Could not sanitize molecule ending on line 2302532
> [13:15:16] ERROR: Explicit valence for atom # 46 N, 4, is greater than
> permitte
> [13:15:16] Explicit valence for atom # 16 N, 4, is greater than permitted
> [13:15:16] ERROR: Could not sanitize molecule ending on line 2302918
> [13:15:16] ERROR: Explicit valence for atom # 16 N, 4, is greater than
> permitte
> [13:15:17] Explicit valence for atom # 11 N, 4, is greater than permitted
> [13:15:17] ERROR: Could not sanitize molecule ending on line 2556541
> [13:15:17] ERROR: Explicit valence for atom # 11 N, 4, is greater than
> permitte
> [13:15:18]  S group SUP ignored on line 2836416
> [13:15:18] Explicit valence for atom # 1 Cl, 4, is greater than permitted
> [13:15:18] ERROR: Could not sanitize molecule ending on line 2841449
> [13:15:18] ERROR: Explicit valence for atom # 1 Cl, 4, is greater than
> permitte
> [13:15:19] Warning: conflicting stereochemistry at atom 10 ignored.
> [13:15:19] Warning: conflicting stereochemistry at atom 10 ignored.
> [13:15:19] Warning: conflicting stereochemistry at atom 17 ignored.
> [13:15:19] Warning: conflicting stereochemistry at atom 17 ignored.
> [13:15:19] Explicit valence for atom # 3 B, 4, is greater than permitted
> [13:15:19] ERROR: Could not sanitize molecule ending on line 3107498
> 

Re: [Rdkit-discuss] SD file read error

[Jan Holst Jensen]

On 2017-01-11 19:26, Milinda Samaraweera wrote:

Dear Experts,

I was trying to read in the attached SD file (downloaded from HMDB) 
and trying to calculate the exact mass of each entry:



​[...]

By running the script, I got a barrage of errors as:

[13:15:14] ERROR: Could not sanitize molecule ending on line 1993855
[13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than 
permitted

[13:15:14] Explicit valence for atom # 9 O, 3, is greater than permitted
[13:15:14] ERROR: Could not sanitize molecule ending on line 1994014
[13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than 
permitted

[13:15:14] Explicit valence for atom # 9 O, 3, is greater than permitted
[13:15:14] ERROR: Could not sanitize molecule ending on line 1996036
[13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than 
permitted

[13:15:16] Explicit valence for atom # 46 N, 4, is greater than permitted
[13:15:16] ERROR: Could not sanitize molecule ending on line 2302532
[13:15:16] ERROR: Explicit valence for atom # 46 N, 4, is greater than 
permitte

[13:15:16] Explicit valence for atom # 16 N, 4, is greater than permitted
[13:15:16] ERROR: Could not sanitize molecule ending on line 2302918
[13:15:16] ERROR: Explicit valence for atom # 16 N, 4, is greater than 
permitte

[13:15:17] Explicit valence for atom # 11 N, 4, is greater than permitted
[13:15:17] ERROR: Could not sanitize molecule ending on line 2556541
[13:15:17] ERROR: Explicit valence for atom # 11 N, 4, is greater than 
permitte

[13:15:18]  S group SUP ignored on line 2836416
[13:15:18] Explicit valence for atom # 1 Cl, 4, is greater than permitted
[13:15:18] ERROR: Could not sanitize molecule ending on line 2841449
[13:15:18] ERROR: Explicit valence for atom # 1 Cl, 4, is greater than 
permitte

[13:15:19] Warning: conflicting stereochemistry at atom 10 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 10 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 17 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 17 ignored.
[13:15:19] Explicit valence for atom # 3 B, 4, is greater than permitted
[13:15:19] ERROR: Could not sanitize molecule ending on line 3107498
[13:15:19] ERROR: Explicit valence for atom # 3 B, 4, is greater than 
permitted

[13:15:19] Warning: conflicting stereochemistry at atom 6 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 6 ignored.
[13:15:20]  Unhandled CTAB feature: S group SRU on line: 3205922. 
Molecule skip

[13:15:20] Explicit valence for atom # 0 Mg, 4, is greater than permitted
[13:15:20] ERROR: Could not sanitize molecule ending on line 3222378
[13:15:20] ERROR: Explicit valence for atom # 0 Mg, 4, is greater than 
permitte

[13:15:20] Explicit valence for atom # 2 N, 4, is greater than permitted
[13:15:20] ERROR: Could not sanitize molecule ending on line 3265386
[13:15:20] ERROR: Explicit valence for atom # 2 N, 4, is greater than 
permitted

[13:15:20] Explicit valence for atom # 31 N, 4, is greater than permitted
[13:15:20] ERROR: Could not sanitize molecule ending on line 3305754
[13:15:20] ERROR: Explicit valence for atom # 31 N, 4, is greater than 
permitte

[13:15:21] Explicit valence for atom # 45 N, 4, is greater than permitted
[13:15:21] ERROR: Could not sanitize molecule ending on line 3437055
[13:15:21] ERROR: Explicit valence for atom # 45 N, 4, is greater than 
permitte

[13:15:56] Explicit valence for atom # 3 C, 5, is greater than permitted
[13:15:56] ERROR: Could not sanitize molecule ending on line 8391489
[13:15:56] ERROR: Explicit valence for atom # 3 C, 5, is greater than 
permitted


What causes these errors? there a way to suppress or solve the errors? 
or way to stop priting them up in the command prompt.


--
Thanks,
Milinda Samaraweera,


Hi Milinda,

The errors are caused by valence errors in the SD file.

> [13:15:14] ERROR: Could not sanitize molecule ending on line 1993855
> [13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than 
permitted


This molecule has a single bond and a double bond to one of the oxygens 
= 3 valences used. Standard valence for uncharged oxygen is 2, so that 
won't work. Given that there is a negatively charged Cl in the molecule 
it is likely that this oxygen should have had a positive charge of one 
assigned. This would make the error go away.


The nitrogens with valence 4 should probably also have a positive charge 
applied - or bond orders adjusted.


> [13:15:56] ERROR: Could not sanitize molecule ending on line 8391489
> [13:15:56] ERROR: Explicit valence for atom # 3 C, 5, is greater than 
permitted


Pentavalent carbon... hmm... could in principle be fixed with a negative 
charge on the carbon, but where is the counterion ?


I would recommend that you leave the error messages turned on - they do 
tell you that there is something wrong with the input structures. But if 
you really want to turn them off there is a discussion about it here:

Re: [Rdkit-discuss] SD file read error

[Steve O'Hagan]

With same code and fresh file download, works fine for me without error.

ms contains 35177 molecules. Perhaps your download was corrupt?

On 11/01/2017 18:26, Milinda Samaraweera wrote:

Dear Experts,

I was trying to read in the attached SD file (downloaded from HMDB) 
and trying to calculate the exact mass of each entry:

​
structures.sdf 


​
from rdkit import Chem
from rdkit.Chem import Descriptors

suppl  = Chem.SDMolSupplier(input_file)

low_mass=50
high_mass=1000

ms = []

for mol in suppl :

if mol is None: continue

try:
if mol and 
round(Descriptors.ExactMolWt(mol),4)>=low_mass and 
round(Descriptors.ExactMolWt(mol),4)<=high_mass:

ms.append(mol)

except:
  pass

By running the script, I got a barrage of errors as:

[13:15:14] ERROR: Could not sanitize molecule ending on line 1993855
[13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than 
permitted

[13:15:14] Explicit valence for atom # 9 O, 3, is greater than permitted
[13:15:14] ERROR: Could not sanitize molecule ending on line 1994014
[13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than 
permitted

[13:15:14] Explicit valence for atom # 9 O, 3, is greater than permitted
[13:15:14] ERROR: Could not sanitize molecule ending on line 1996036
[13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than 
permitted

[13:15:16] Explicit valence for atom # 46 N, 4, is greater than permitted
[13:15:16] ERROR: Could not sanitize molecule ending on line 2302532
[13:15:16] ERROR: Explicit valence for atom # 46 N, 4, is greater than 
permitte

[13:15:16] Explicit valence for atom # 16 N, 4, is greater than permitted
[13:15:16] ERROR: Could not sanitize molecule ending on line 2302918
[13:15:16] ERROR: Explicit valence for atom # 16 N, 4, is greater than 
permitte

[13:15:17] Explicit valence for atom # 11 N, 4, is greater than permitted
[13:15:17] ERROR: Could not sanitize molecule ending on line 2556541
[13:15:17] ERROR: Explicit valence for atom # 11 N, 4, is greater than 
permitte

[13:15:18]  S group SUP ignored on line 2836416
[13:15:18] Explicit valence for atom # 1 Cl, 4, is greater than permitted
[13:15:18] ERROR: Could not sanitize molecule ending on line 2841449
[13:15:18] ERROR: Explicit valence for atom # 1 Cl, 4, is greater than 
permitte

[13:15:19] Warning: conflicting stereochemistry at atom 10 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 10 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 17 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 17 ignored.
[13:15:19] Explicit valence for atom # 3 B, 4, is greater than permitted
[13:15:19] ERROR: Could not sanitize molecule ending on line 3107498
[13:15:19] ERROR: Explicit valence for atom # 3 B, 4, is greater than 
permitted

[13:15:19] Warning: conflicting stereochemistry at atom 6 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 6 ignored.
[13:15:20]  Unhandled CTAB feature: S group SRU on line: 3205922. 
Molecule skip

[13:15:20] Explicit valence for atom # 0 Mg, 4, is greater than permitted
[13:15:20] ERROR: Could not sanitize molecule ending on line 3222378
[13:15:20] ERROR: Explicit valence for atom # 0 Mg, 4, is greater than 
permitte

[13:15:20] Explicit valence for atom # 2 N, 4, is greater than permitted
[13:15:20] ERROR: Could not sanitize molecule ending on line 3265386
[13:15:20] ERROR: Explicit valence for atom # 2 N, 4, is greater than 
permitted

[13:15:20] Explicit valence for atom # 31 N, 4, is greater than permitted
[13:15:20] ERROR: Could not sanitize molecule ending on line 3305754
[13:15:20] ERROR: Explicit valence for atom # 31 N, 4, is greater than 
permitte

[13:15:21] Explicit valence for atom # 45 N, 4, is greater than permitted
[13:15:21] ERROR: Could not sanitize molecule ending on line 3437055
[13:15:21] ERROR: Explicit valence for atom # 45 N, 4, is greater than 
permitte

[13:15:56] Explicit valence for atom # 3 C, 5, is greater than permitted
[13:15:56] ERROR: Could not sanitize molecule ending on line 8391489
[13:15:56] ERROR: Explicit valence for atom # 3 C, 5, is greater than 
permitted


What causes these errors? there a way to suppress or solve the errors? 
or way to stop priting them up in the command prompt.


--
Thanks,
Milinda Samaraweera,



--
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi


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[Rdkit-discuss] SD file read error

[Milinda Samaraweera]

Dear Experts,

I was trying to read in the attached SD file (downloaded from HMDB) and
trying to calculate the exact mass of each entry:
​
 structures.sdf

​
from rdkit import Chem
from rdkit.Chem import Descriptors

suppl  = Chem.SDMolSupplier(input_file)

low_mass=50
high_mass=1000

ms = []

for mol in suppl :

if mol is None: continue

try:
if mol and round(Descriptors.ExactMolWt(mol),4)>=low_mass
andround(Descriptors.ExactMolWt(mol),4)<=high_mass:
ms.append(mol)

except:
  pass

By running the script, I got a barrage of errors as:

[13:15:14] ERROR: Could not sanitize molecule ending on line 1993855
[13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than
permitted
[13:15:14] Explicit valence for atom # 9 O, 3, is greater than permitted
[13:15:14] ERROR: Could not sanitize molecule ending on line 1994014
[13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than
permitted
[13:15:14] Explicit valence for atom # 9 O, 3, is greater than permitted
[13:15:14] ERROR: Could not sanitize molecule ending on line 1996036
[13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than
permitted
[13:15:16] Explicit valence for atom # 46 N, 4, is greater than permitted
[13:15:16] ERROR: Could not sanitize molecule ending on line 2302532
[13:15:16] ERROR: Explicit valence for atom # 46 N, 4, is greater than
permitte
[13:15:16] Explicit valence for atom # 16 N, 4, is greater than permitted
[13:15:16] ERROR: Could not sanitize molecule ending on line 2302918
[13:15:16] ERROR: Explicit valence for atom # 16 N, 4, is greater than
permitte
[13:15:17] Explicit valence for atom # 11 N, 4, is greater than permitted
[13:15:17] ERROR: Could not sanitize molecule ending on line 2556541
[13:15:17] ERROR: Explicit valence for atom # 11 N, 4, is greater than
permitte
[13:15:18]  S group SUP ignored on line 2836416
[13:15:18] Explicit valence for atom # 1 Cl, 4, is greater than permitted
[13:15:18] ERROR: Could not sanitize molecule ending on line 2841449
[13:15:18] ERROR: Explicit valence for atom # 1 Cl, 4, is greater than
permitte
[13:15:19] Warning: conflicting stereochemistry at atom 10 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 10 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 17 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 17 ignored.
[13:15:19] Explicit valence for atom # 3 B, 4, is greater than permitted
[13:15:19] ERROR: Could not sanitize molecule ending on line 3107498
[13:15:19] ERROR: Explicit valence for atom # 3 B, 4, is greater than
permitted
[13:15:19] Warning: conflicting stereochemistry at atom 6 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 6 ignored.
[13:15:20]  Unhandled CTAB feature: S group SRU on line: 3205922. Molecule
skip
[13:15:20] Explicit valence for atom # 0 Mg, 4, is greater than permitted
[13:15:20] ERROR: Could not sanitize molecule ending on line 3222378
[13:15:20] ERROR: Explicit valence for atom # 0 Mg, 4, is greater than
permitte
[13:15:20] Explicit valence for atom # 2 N, 4, is greater than permitted
[13:15:20] ERROR: Could not sanitize molecule ending on line 3265386
[13:15:20] ERROR: Explicit valence for atom # 2 N, 4, is greater than
permitted
[13:15:20] Explicit valence for atom # 31 N, 4, is greater than permitted
[13:15:20] ERROR: Could not sanitize molecule ending on line 3305754
[13:15:20] ERROR: Explicit valence for atom # 31 N, 4, is greater than
permitte
[13:15:21] Explicit valence for atom # 45 N, 4, is greater than permitted
[13:15:21] ERROR: Could not sanitize molecule ending on line 3437055
[13:15:21] ERROR: Explicit valence for atom # 45 N, 4, is greater than
permitte
[13:15:56] Explicit valence for atom # 3 C, 5, is greater than permitted
[13:15:56] ERROR: Could not sanitize molecule ending on line 8391489
[13:15:56] ERROR: Explicit valence for atom # 3 C, 5, is greater than
permitted

What causes these errors? there a way to suppress or solve the errors? or
way to stop priting them up in the command prompt.

-- 
Thanks,
Milinda Samaraweera,
--
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi___
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