From NWChem
Viewed 1566 times, With a total of 1 Posts
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Posts 17
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| 1:15:18 PM PDT - Sun, Jul 22nd 2012 |
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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!
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Edited On 1:09:09 AM PDT - Mon, Jul 23rd 2012 by Yjleedaniel
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Clicked A Few Times
Threads 5
Posts 17
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| 1:07:18 AM PDT - Mon, Jul 23rd 2012 |
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the solution was very simple
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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?
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Edited On 1:10:32 AM PDT - Mon, Jul 23rd 2012 by Yjleedaniel
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