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I started to optimise a selected cavity of the enzyme with a metal ion using Gaussian 09 software. The basis set used for C,H,N and O atoms was 6-311+G(d) and for the Cd2+ ion was def2-tzvp. And, after few seconds of the Gaussian calculation, the job terminates with the memory error. Then I tried the suggested solution of using "%mem=1043MW" . But that did not work and the Gaussian run terminated after reading the coordinates and no error was mentioned. How can I solve this issue and what might be the reason for this, any wrong in the method? I have attached the link to my Gaussian files here.

In preparing the input file I have included the all the hydrogen atoms.

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    $\begingroup$ Can you post the input and the error using the code block? $\endgroup$ Feb 11, 2023 at 10:00
  • $\begingroup$ @AndreaPellegrini I am so sorry.. since I am new to this platform I have no idea on how to include my input because I tried editing my original post but then it came up with a message of exceeding character limit. So could you please guide me in posting the files. And sorry once again for the trouble. $\endgroup$
    – PriZarah
    Feb 11, 2023 at 10:59
  • $\begingroup$ If including the input and errors causes the post to exceed the character limit, then please add them to the Modeling Matters GitHub repository in a folder called 10402 since that's the number in this question's URL. $\endgroup$ Feb 11, 2023 at 11:43
  • $\begingroup$ This seems to be a duplicate of this prior question which was closed for not responding to requests for clarification. Both of these questions and your other questions on the site seem to be related to a particular systems. Several users have commented with suggestions or requests for clarification from you, but received no response. Please try to include these details in your question and try these suggestions, explaining why they did/didn't work for you. We can only help if we fully understand the problem. $\endgroup$
    – Tyberius
    Feb 11, 2023 at 12:30
  • $\begingroup$ @Tyberius we find ourselves explaining the same thing repeatedly sometimes: in this case it's the fact that the input/output files are hosted by Google Drive, which is not available in some countries, and has the disadvantage that people visiting the site several years from now will no longer be able to see the file (making the question "obsolete" in a sense). From now on we can just point users to this Meta post instead of explaining it every time. $\endgroup$ Feb 11, 2023 at 14:33

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I tried to solve the problem. Here what I did. In the input, the first part, try to select the number of CPU or Gaussian will take the default=1, and in your case you need a lot of CPUs as you can because it is huge system.

%chk=pk(i).chk
%mem=100GB
%nproc=20
# opt b3lyp/3-21g geom=connectivity

The last part of the input. I just defined the basis set for Cd2+ ions.

C 0
6-311+G(d)
****
N 0
6-311+G(d)
****
O 0
6-311+G(d)
****
H 0
6-311+G(d)
****
Cd 0
DEF2TZVP
****

Cd 0
DEF2TZVP

If it is ok for you in this way, the calculation is running well, but it will take time. Here is part of the output.

 HarFok:  IExCor=  402 AccDes= 0.00D+00 IRadAn=         5 IDoV= 1 UseB2=F ITyADJ=14
 ICtDFT=  3500011 ScaDFX=  1.000000  1.000000  1.000000  1.000000
 Defaulting to unpruned grid for atomic number  48.
 FoFCou: FMM=F IPFlag=           0 FMFlag=      100000 FMFlg1=        2001
         NFxFlg=           0 DoJE=T BraDBF=F KetDBF=T FulRan=T
         wScrn=  0.000000 ICntrl=       500 IOpCl=  0 I1Cent=   200000004 NGrid=           0
         NMat0=    1 NMatS0=      1 NMatT0=    0 NMatD0=    1 NMtDS0=    0 NMtDT0=    0
 Petite list used in FoFCou.
 Initial guess <Sx>= 0.0000 <Sy>= 0.0000 <Sz>= 0.5000 <S**2>= 0.7500 S= 0.5000
 Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
 Requested convergence on MAX density matrix=1.00D-06.
 Requested convergence on             energy=1.00D-06.
 No special actions if energy rises.
 CoulSu:  requested number of processors reduced to:  17 ShMem   1 Linda.
 CalDSu:  requested number of processors reduced to:  17 ShMem   1 Linda.
 Defaulting to unpruned grid for atomic number  48.
 CoulSu:  requested number of processors reduced to:  17 ShMem   1 Linda.
 CalDSu:  requested number of processors reduced to:  17 ShMem   1 Linda.
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  • $\begingroup$ Thank you @Abd-Elazeem Mohamed for the answer. But I have the problem with memory. So I thought to do this using two layer calculation and go with a lower basis set for low layer atoms. $\endgroup$
    – PriZarah
    Mar 8, 2023 at 10:36

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