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#37156 - 09/19/18 02:04 AM Some test codes were not performed.
SDUM Offline
Forum Member

Registered: 09/18/18
Posts: 2
Loc: Japan
Hi everyone,

I read this article (https://www.nature.com/articles/ncomms15443) and I want to try the Action-CSA method.
In "Data availability", it is written that the Action-CSA code is freely available as a part of the CHARMM molecular dynamics package.

I just installed charmm with the command "./install.com gnu M".
Then I checked the /test/c36test directory after executing "./test.com gnu M 2" and read csatest.inp and csamin.inp in order to understand how to use CSA method.
However, these tests were not performed with the following message:

-----------
Maximum number of ATOMS: 360720, and RESidues: 120240
RDTITL> * CHARMM 36 TESTCASE CSATEST.INP
RDTITL> * TEST THE CSA MODULE
RDTITL> * AUTHOR: MILAN HODOSCEK
RDTITL> * THE SYSTEM OBTAINED FROM:
RDTITL> * WIKIPEDIA: TETRAPEPTIDE -> THE FIRST ON THE LIST
RDTITL> *

CHARMM>

CHARMM> if ?distene .ne. 1 then
RDCMND: can not substitute energy "?DISTENE"
Comparing "?DISTENE" and "1".
IF test evaluated as true. Performing command

CHARMM> echo "csatest.inp> Test NOT performed."
"csatest.inp> Test NOT performed."

CHARMM> stop
$$$$$$ New timer profile $$$$$
Total time 0.03 Other: 0.00

NORMAL TERMINATION BY NORMAL STOP
NO WARNINGS WERE ISSUED

$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 0.03 SECONDS
CPU TIME: 0.03 SECONDS

-----------

What is "distene" in this message and why is this test not performed?
What should I do to perform these tests and CSA calculation?

thanks

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#37157 - 09/19/18 11:52 AM Re: Some test codes were not performed. [Re: SDUM]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8406
Loc: 39 03 48 N, 77 06 54 W
It is difficult to give any advice, as the CSA developers appear to have done a Very Bad Job as far as documenting how to compile the CSA code, and how to use it.

I suspect this may be somewhat immature code; you could try contacting the first author (Juyong Lee).
_________________________
Rick Venable
computational chemist


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#37160 - 09/20/18 01:43 AM Re: Some test codes were not performed. [Re: SDUM]
SDUM Offline
Forum Member

Registered: 09/18/18
Posts: 2
Loc: Japan
Rick,
Thanks a lot for your advice!
I intend to try it.


Edited by SDUM (09/20/18 01:44 AM)

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