(Solved) (prepare task for qmmm) nwchem omits a atom

From NWChem

Viewed 1649 times, With a total of 1 Posts
Jump to: navigation, search

Clicked A Few Times
Threads 5
Posts 17
Hello, everyone.

I'm trying to make a water solvation box with prepare task. There is a lithium atom in my system.

The problem is that, there is no lithium atom in the result pdb file, after I do the prepare task.



I wrote the lithium in the source pdb file like this. Here, segment 1 is used for the other molecule.
ATOM     17  LI  1Li     1       0.001   0.001   0.001

for the segment2 part of output script (of prepare task) is like this.
Creating fragment for residue 1Li     

Atom type definitions /opt/nwchem/nwchem-6.0-install/data/amber_s/amber.par
Atom type definitions /opt/nwchem/nwchem-6.0-install/data/amber_q/amber.par
Atom type definitions /opt/nwchem/nwchem-6.0-install/data/amber_x/amber.par
Bond charge definitions /opt/nwchem/nwchem-6.0-install/data/amber_s/amber.par
Bond charge definitions /opt/nwchem/nwchem-6.0-install/data/amber_q/amber.par
Bond charge definitions /opt/nwchem/nwchem-6.0-install/data/amber_x/amber.par

Fragment 1Li

num name type link cntr grp pgrp charge polarizab

------------
total charge 0.000000

There should be some information about lithium atom below the
 num name  type   link cntr  grp pgrp    charge     polarizab
line, isn't it?


Did I wrote something wrong in source pdb file? Can you help me...? Thanks a lot in advance!
Edited On 1:09:09 AM PDT - Mon, Jul 23rd 2012 by Yjleedaniel

Clicked A Few Times
Threads 5
Posts 17
the solution was very simple
name of atom was the problem.

There should be a number so that the name is like "LI1"
"LI1" (all capital) and "Li1" is OK, but "li1" (all lower case) or "Li" (no number) didn't work.

Also, I found that the residue name ("1Li" in this case) is not the matter.


Where can I get these kind of information??? The solution is very simple but I took quite much time to find it.
Am I the only one who don't know such things?
Edited On 1:10:32 AM PDT - Mon, Jul 23rd 2012 by Yjleedaniel


Forum >> NWChem's corner >> QMMM



Who's here now Members 0 Guests 0 Bots/Crawler 1


AWC's: 2.5.10 MediaWiki - Stand Alone Forum Extension
Forum theme style by: AWC