Dear Junbo,
Without knowing i) which version of Amber you are using, ii) how you changed the code and iii) the error message that you get, it is hard to help. Please be more specific.
For lanthanides it might be sufficient to extend qmmm_module.F90. For actinides, elementOrbitalIndex.F90 also requires updates; other files possibly, too. This all assumes that you want to use an external QM code and not the semiempirical QM methods that are native to Amber.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Project Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
> On Mar 13, 2017, at 7:22 PM, 鲁俊波 <lujb15.mails.tsinghua.edu.cn> wrote:
>
> Dear all AMBER experts:
>
> I want to do the QM/MM MD simulation for my system containing lanthanide elements. But I find that AMBER can not recognize the lanthanide elements, also it can not recognize the actinide elements. I check the source code, and I search some code of qmmm_module.F90 in sqm directory:
>
> ! Lanthanides are not supported.
> ! Actinides are not supported.
>
> if( Upcase(atom_name(1:1)) .eq. 'A' ) then
> if(atom_mass > 24.0d0 .and. atom_mass <= 28.0d0) then
> atomic_number = 13 !Aluminium
> elseif(atom_mass > 35.0d0 .and. atom_mass <= 40.0d0) then
> atomic_number = 18 !Argon
> elseif(atom_mass > 73.0d0 .and. atom_mass <= 77.0d0) then
> atomic_number = 33 !Arsenic
> elseif(atom_mass > 106.0d0 .and. atom_mass <= 109.0d0) then
> atomic_number = 47 !Silver
> elseif(atom_mass > 195.0d0 .and. atom_mass <= 199.0d0) then
> atomic_number = 79 !Gold
> elseif(atom_mass > 208.0d0 .and. atom_mass <= 212.0d0) then
> atomic_number = 85 !Astatine
> else
> localErrorFlag=.true.
> endif
>
> ......
>
> Then I try to change some code to make sure AMBER can recognize the lanthanide and actinide elements. But it can not work. Can anyone give me a help about the QM/MM MD simulation for the system containing lanthanide and actinide elements? I will be very appreciated!
>
> With my best regards,
>
> Junbo
>
>
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Received on Mon Mar 13 2017 - 21:00:03 PDT
