how to prepare QM/MM calculations from scratch

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  • Marat Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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I have added new section on how to prepare QM/MM calculations from scratch in http://www.nwchem-sw.org/index.php/QMMM_Appendix#Preparing_QM.2FMM_calculations_from_scrat...

Marat

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How are we going to deal with a bigger system?
Hi Marat,

I went through the example of QMMM preparation from scratch. It still seems a little bit chanllenging to me. I was trying to prepare a QMMM simulation for our system, which has over 200 residues and some DNA fragments with its quantum treated part scattered across a few different residues and dna bases. I tried to run the prepare module with only one atom treated as quatum part (just for test), it generated a lot of .frg_TMP files. I am not sure how can I start from there. Am I suppose to modify all of the .frg_TMP files? Is there any possibility that you can include a more complex example on the website? Your help will be greatly appreicated!

Sincerely
Xiaojun Xu

  • Marat Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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NWChem comes with all the standard amino acid residue fragments and nucleotides, which covers many biological systems. I suspect that there is something wrong with your .nwchemrc file which specifies the location of these fragments and parameter files. Here is an example of my .nwchemrc file (your paths would be different if course)


  nwchem_basis_library /Users/marat/opt/codes/nwchem-new/src/basis/libraries/
ffield amber

  amber_1   /Users/marat/opt/codes/nwchem-new/src/data/amber_s/
amber_2 /Users/marat/opt/codes/nwchem-new/src/data/amber_q/
amber_3 /Users/marat/opt/codes/nwchem-new/src/data/amber_x/
amber_4 /Users/marat/opt/codes/nwchem-new/src/data/amber_u/
spce /Users/marat/opt/codes/nwchem-new/src/data/solvents/spce.rst
thfs /Users/marat/opt/codes/nwchem-new/src/data/solvents/thfs.rst
charmm_s /Users/marat/opt/codes/nwchem-new/src/data/charmm_s/
charmm_x /Users/marat/opt/codes/nwchem-new/src/data//charmm_x/

Marat
Edited On 11:29:54 AM PST - Fri, Dec 9th 2011 by Marat

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Hi Marat,

Thanks a lot for your reply! I actaully did not use a general site installation. The program was installed in my home directory. When I looked for the .nwchemrc file, I found there was no /data dirctory in the /nwchem-6.0 dirctory, I was not sure whether this was a problem due to my installation. Then I went ahead created a /data directory and copied everything required into it, and created a .nwchemrc file in it, with the specified paths. However, the program still generated a lot of .frg_TMP files as it used to do. What could possible be the problem?

Xiaojun
Edited On 2:23:34 PM PST - Mon, Dec 12th 2011 by Maxabruzzi

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Quote:Marat Nov 29th 2:15 pm
I have added new section on how to prepare QM/MM calculations from scratch in http://www.nwchem-sw.org/index.php/QMMM_Appendix#Preparing_QM.2FMM_calculations_from_scrat...

Marat


Hi Marat,

I followed the example step by step. Although I created the NN3.frg file, the program still generates the same error as before generating NN3.frg : Unresolved atom types in fragment NN3. Do you know what the origin of the error is?

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Quote:Hassan Aug 20th 2:05 pm
Quote:Marat Nov 29th 2:15 pm
I have added new section on how to prepare QM/MM calculations from scratch in http://www.nwchem-sw.org/index.php/QMMM_Appendix#Preparing_QM.2FMM_calculations_from_scrat...

Marat


Hi Marat,

I followed the example step by step. Although I created the NN3.frg file, the program still generates the same error as before generating NN3.frg : Unresolved atom types in fragment NN3. Do you know what the origin of the error is?


Hi Hassan,

This may because you have not set the .nwchemrc file. I encountered the same problem and went through the example by setting .nwchemrc file correct.

wjb0920

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Quote:Wjb0920 Aug 23rd 2:37 am
Quote:Hassan Aug 20th 2:05 pm
Quote:Marat Nov 29th 2:15 pm
I have added new section on how to prepare QM/MM calculations from scratch in http://www.nwchem-sw.org/index.php/QMMM_Appendix#Preparing_QM.2FMM_calculations_from_scrat...

Marat


Hi Marat,

I followed the example step by step. Although I created the NN3.frg file, the program still generates the same error as before generating NN3.frg : Unresolved atom types in fragment NN3. Do you know what the origin of the error is?


Hi Hassan,

This may because you have not set the .nwchemrc file. I encountered the same problem and went through the example by setting .nwchemrc file correct.

wjb0920


Hi,
Thanks. You are right. Now it works!


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