problems defining QM region
Just Got Here
4:45:33 AM PDT - Thu, Jun 5th 2014
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

Just Got Here
6:23:24 AM PDT - Thu, Jun 5th 2014
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

Just Got Here
5:49:54 AM PDT - Fri, Jun 6th 2014
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.

Clicked A Few Times
12:32:35 AM PDT - Tue, Sep 23rd 2014
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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