Atoms Are Too Close, Please Check your Geometry Input

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Just Got Here
Threads 1
Posts 4
Hi everyone. I'm new to NWChem and I'm trying to run a .nw file with the dplot command. I have attached the .nw script file here -> https://pastebin.com/qKWf9wFZ

I get the following error when I run my code:

"
minimum distance 3.4380551002623154e-002
                  • warning********
at least two atoms are only 0.018 angstrom apart
Please check your geometry input
                  • warning********
If you like danger & want to skip this check
add the following input line
set geom:dont_verify .true.


geom_input: geom_verify_coords failed 911


current input line:
3693: end




There is an error related to the specified geometry


"

I got the geometrical atoms/structure information from Avagadro's ability to "Fetch from PDB" of 3szt (PDB's name for QscR). It has 3,690 atoms.

I followed the instructions mentioned at http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id1106/NWChem_for_Large_systems.htm... to be able to work with structures that has greater than 3,000 atoms (usually the default of nwchem).

Thank you for the help!

Forum Regular
Threads 1
Posts 190
As the error says, you have atoms that are too close together. This is easy to see if you visualize your system. Look up the occupancy keyword for PDB files to understand why you have atoms really close to each other. Also, your system has no hydrogen atoms (common for PDB files not to include hydrogen atoms), so you will need to add those as well if you want any chance of converging the SCF.

Just Got Here
Threads 1
Posts 4
geom_input: autosym bug : too few atoms
So, after adding Hydrogen atoms I ran into this new error (please see below in the " " section) in NWChem. So, now I have too few atoms.

I used http://molprobity.biochem.duke.edu/ to add the hydrogen atoms, and then used Avagadro to generate the chemical structure NWChem file. NOTE: I added " set geom:dont_verify .true. " into the .nw file. Whether it is there or not, I still get the same error that is shown below.

The following link can be used to see my new .nw file.

https://pastebin.com/hkggvpaZ

"

geom_input: autosym bug : too few atoms 7294
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
7300: end
------------------------------------------------------------------------
------------------------------------------------------------------------
There is an error related to the specified geometry
------------------------------------------------------------------------
For more information see the NWChem manual at http://www.nwchem-sw.org/index.php/NWChem_Documentation


For further details see manual section:                                                                                                                                                                                                                                                                
0:0:geom_input: autosym bug : too few atoms:: 7294
(rank:0 hostname:hunt-P10S-M-WS-Series pid:13768):ARMCI DASSERT fail. ../../ga-5-4/armci/src/common/armci.c:ARMCI_Error():208 cond:0
Last System Error Message from Task 0:: No such file or directory

"

Forum Regular
Threads 1
Posts 190
Try turning off autosym

Just Got Here
Threads 1
Posts 4
So, after adding the hydrogens to my PDB-downloaded-structure AND turning off autosym, I try to run dplot with my file (here https://pastebin.com/Dv8ade6y ). However, I still get the error shown here https://pastebin.com/0Rtm3JeD .

Any help would be greatly appreciated! Thank you!

Forum Vet
Threads 12
Posts 1675
The input file you have uploaded does not contain the noautosym keyword suggested by Sean
https://github.com/nwchemgit/nwchem/wiki/Geometry

By the way, the autosym process fails because the distances between atoms 5299 and 5300, 5303 and 5304, 5317 and 5318, 5319 and 5320, 5321 and 5322, 5327 and 5328, 6135 and 6136, etc ... are less than 0.5 angstroms. You might want to avoid this state of affairs
Edited On 5:48:49 PM PDT - Wed, Apr 25th 2018 by Edoapra

Just Got Here
Threads 1
Posts 4
@Edoapara

Thank you for the clarification about autosym.
Do you have any suggestions on how I may avoid those state of affairs that you mentioned. I'm not sure how to, given that that's the geometrical structure of the protein I'm trying to work with.

Thank you!

Forum Regular
Threads 1
Posts 190
As I said before, you have atoms too close together because of the occupancy field in the PDB file. To quote the Guide to Understanding PDB Data (https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/dealing-with-coordinates):

"Macromolecular crystals are composed of many individual molecules packed into a symmetrical arrangement. In some crystals, there are slight differences between each of these molecules. For instance, a sidechain on the surface may wag back and forth between several conformations, or a substrate may bind in two orientations in an active site, or a metal ion may be bound to only a few of the molecules. When researchers build the atomic model of these portions, they can use the occupancy to estimate the amount of each conformation that is observed in the crystal. For most atoms, the occupancy is given a value of 1, indicating that the atom is found in all of the molecules in the same place in the crystal. However, if a metal ion binds to only half of the molecules in the crystal, the researcher will see a weak image of the ion in the electron density map, and can assign an occupancy of 0.5 in the PDB structure file for this atom. Occupancies are also commonly used to identify sidechains or ligands that are observed in multiple conformations. The occupancy value is used to indicate the fraction of molecules that have each of the conformations. Two (or more) atom records are included for each atom, with occupancies like 0.5 and 0.5, or 0.4 and 0.6, or other fractional occupancies that sum to a total of 1."

To resolve this you need to look for a script/program someone else has written to automatically extract just one of the positions for atoms with occupancy less than 1, write a script yourself to do it, or manually delete the duplicated atoms from your input. In doing this manually, NWChem could be used as a guide since the code will tell you which atoms are too close to each other.


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