From NWChem
Viewed 1803 times, With a total of 3 Posts
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Just Got Here
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| 4:45:33 AM PDT - Thu, Jun 5th 2014 |
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Dear Nwchem users,
I prepared a simple QM/MM optimization input, where only an aspartate side chain was included in the QM part. The prepare module looks like:
prepare
system spl
source prot.pdb
amber
new_top new_seq
new_rst
modify atom 123:_CB quantum
modify atom 123:2HB quantum
modify atom 123:3HB quantum
modify atom 123:_CG quantum
modify atom 123:_OD1 quantum
modify atom 123:_OD2 quantum
center
orient
solvate
update lists
ignore
write spl_ref.rst
write spl_ref.pdb
end
task prepare
I think the definitions of the QM atoms are as in the example inputs, and in fact they are accepted as QM atoms. However, when I check the pdb file created, the two HB atoms are placed far away from their original positions (the remaining QM atoms are OK). If I remove the two H atoms from the QM part, then they location is correct. I appreciate if someone could explain the reason for this.
Thanks
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Just Got Here
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| 6:23:24 AM PDT - Thu, Jun 5th 2014 |
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It's me again.
I managed to set up the geometry correctly, after removing "update lists". However, I think this is an important keyword. I would appreciate if someone could explain why this keyword has such effects on the geometry, and, if its deletion may have critical consequences on the final results.
Thanks
Jon
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Just Got Here
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Posts 3
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| 5:49:54 AM PDT - Fri, Jun 6th 2014 |
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Just to complete the story... I solved the problem.
The point is that I am importing the source pdb from Gromacs, and the hydrogen atom names do not match with Nwchem's. When the system is set up, the program complains about some of these names, but not about HB hydrogens. However, if they are included in the QM part, the problem I posted before arises. The solution is to update the name of these atoms to Nwchem's.
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Clicked A Few Times
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Posts 8
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| 12:32:35 AM PDT - Tue, Sep 23rd 2014 |
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Hi Pobmugoj,
Thank you for providing the solution to the problem. I have met the similar problem when I run lithium chloride hydrate. I defined the QM atoms and they are accepted as QM atoms. However, when I check the active.pdb file created, the li and Cl atoms are placed far away from their original positions (the remaining QM atoms are OK). As you reported, I remove the li and Cl atoms from the QM part, or remove "update lists". Unfortunately, the li and Cl atoms are still placed far away from their original positions. And I think the two atom names match with Nwchem's .I would like to povide any files . Could you offer me some advice?Thanks a lot.
zhangll
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