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#36016 11/10/16 10:43 PM
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Greetings, I am new here and a graduate student studying biophysics. I am learning MD simulation techniques, and I have a decent experience with CHARMM now. This is a question for those who are experienced with QM/MM in CHARMM. Which interface would you recommend that I learn? I have been researching Gaussian09, QCHEM, and GAMESS. What would you recommend to me as a grad student learning this for the first time? I have some experience with Gaussian09 and enjoy it, but I would like to know what you think. Thanks!

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I believe the Q-Chem interface may be preferred; I know it's used a lot in our lab, and may be the best supported.


Rick Venable
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Great, thanks for the response. I will look into Q-Chem. Another question I have is, maybe, someone could point me in the right direction for doing QM/MM. My first project is to work with divalent copper in a certain ion channel. I've parameterized divalent copper in CHARMM, but of course that isn't very accurate, modeling divalent copper as a spherical ion. We would like to model a certain region of the ion channel as QM and the divalent copper as QM for accurate interactions, but make the rest of the system just MM. Could someone point me in the right direction for tutorials/scripts/examples for doing something like this. Thanks!

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Hi,
Everyone
I am going to interface g09 with C42b1 .I have installed the C42b1 by using the command ./install.com gnu C42b1 g09 .But when I am testing the alanine_g09.inp ,can't get any output for g09
along with for C42b1 .Where I am wrong ?Can any any one Guess ?But when I am omitting the line " if g09 .ne. 1 then stop " in the inputfile then getting the some output file with abnormal termination . Is there any problem to set the environment comment for g09 ?My g09 package is in "root ~/opt " dicrectory .I am using the system CentOS release 6.5 and x86_64 GNU/Linux. I am requeting to post the actual output file of alanine_g09.inp .

My output file is like that

Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Free Version 42b1 August 15, 2017
654
Copyright(c) 1984-2014 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-2.6.32-431.el6.x86_64(x86_64)@ethene
Created on 12/22/17 at 0:22:58 by user: prabhash

Maximum number of ATOMS: 360720, and RESidues: 120240
RDTITL> * CHARMM / G09 TESTCASE CQUANTUMTEST/ALANINE_G09.INP
RDTITL> * AUTHOR: PAUL SHERWOOD (MODIFED FOR Q-CHEM BY H. LEE WOODCOCK)
RDTITL> * MODIFIED FOR GAUSSIAN09 BY MICHAEL GAUS
RDTITL> * ALALNINE TEST CASE FOR QM(G09)/MM USING G09 INTERFACE
RDTITL> * CTERM IS QM AND THE REST IS MM LINK ATOM IS BETWEEN CA AND C
RDTITL> *

CHARMM>

CHARMM> if g09 .ne. 1 then stop
Comparing "G09" and "1".
IF test evaluated as true. Performing command
$$$$$$ New timer profile $$$$$
Total time 0.05 Other: 0.00

NORMAL TERMINATION BY NORMAL STOP
NO WARNINGS WERE ISSUED

$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 0.05 SECONDS
CPU TIME: 0.05 SECONDS
~

Thanks to all.

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rmv Online Content
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The message indicates that CHARMM was not compiled with the G09 keyword. If you include the PREF keyword in CHARMM input, the program will list any special features such as G09.

Perhaps your compile attempt did not succeed; did you check the log files after the build?

The correct syntax is

./install.com gnu G09

Be sure to clean up first by doing the following:
  • Rename (via mv) or delete (rm) exec/gnu/charmm
  • rm -rf lib/gnu build/gnu

If you have a working executable you want to keep, you should rename it. The directory deletion gets rid of debris from previous attempts, which can create conflicts.


Rick Venable
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Hi,
Rick sir

I have followed your above instruction to install the C42b1 to interface with G09 .But I have got the error in /build/gnu/gnu.log file . Some of the last line are like that
/opt/charmm/lib/gnu/nbonds.a(ewald.o): In function `__ewald_MOD_kspace':
ewald.F90:(.text+0x4622): undefined reference to `getgrdq_'
collect2: error: ld returned 1 exit status
make: *** [/opt/charmm/exec/gnu/charmm] Error 1
How can I remove the problem ?

Last edited by prabhash; 12/23/17 09:59 AM.
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rmv Online Content
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Unfortunately, it appears to be a bug in the Ewald code related to G09, so there is no quick answer.


Rick Venable
computational chemist


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