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Error in type "brae" mass '78.918300' not found in map
#37703 11/18/19 07:22 AM
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Hello,

Recently we combine the chemshell 3.6.0 software and charmm 42b2 to generate the charges of all atoms and groups used in subsequent qm/mm cutoff. When we execute the script attached in the .zip file, we found an error as below:
--------------------------------------------------------------------
Initialising ChemShell 3.6.0 on linux
charmm.preinit/================================== Tstep: 0.0 Ttot: 0.0 ==

Initiating Charmm
Setting precision to 17 d.p.

__Level 1__
/ \ #====================> charmm_init

Charmm(scratch) exists - leaving as './'
Charmm(exec) exists - leaving as 'charmm'
Charmm(out) set to - './/outpipe'
Charmm(list) set to - './/charmm.log'
Charmm(make_pipe) set to mknod $name p
Performing 'mknod .//outpipe p' in shell
Launching Charmm

############################
##### #####
##### Charmm Initiated #####
##### #####
############################

Installing Default atom map

__Level 2__
/ \ #====================> charmm_map

Loading default mapping data structure

\__Level 2__/


\__Level 1__/

Waiting for Charmm
==================
==================
For 0.371 scnds
charmm.preinit/charmm_import/==================== Tstep: 0.4 Ttot: 0.4 ==

__Level 2__
/ \ #====================> charmm_get_parameters

'parameters' set to 'natom'
Aquiring parameters
natom -> 15955

\__Level 2__/

ERROR ==> type 'brae' mass '78.918300' not found in map
importing 15955 atoms from CHARMM

Timing Analysis by Executable
ChemShell 0.900 100.0%

Total 0.900

Timing Analysis by Module module # calls time time (exc) percent
Other 0.900 100.0%

Total 0.900
ChemShell exiting code 0
the following objects are still declared:

* dky.c fragment 1 main CHARMM import
writing persistent objects to disk..
done
----------------------------------------------------------------
In our system, 'brae' refers to the bromine. In the prm and rtf file, all of the information of "brae" exist. Have you ever met this above error? Or what is the meaning for "type 'brae' mass '78.918300' not found in map"? The mass of 'brae'clearly exists. Can you help me solve this problem? Thank you so much!


best wishes,
Tyrion

Attached Files
8-selectivate.zip (1.1 MB, 93 downloads)
Re: Error in type "brae" mass '78.918300' not found in map
tyrion_jj #37704 11/18/19 04:52 PM
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Posts: 8,501
rmv Online Content
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None of the messages posted appear to be from CHARMM, and there are no error or warning indications in the charmm.log file.


Rick Venable
computational chemist

Re: Error in type "brae" mass '78.918300' not found in map
rmv #37707 11/19/19 06:45 AM
Joined: Jan 2019
Posts: 21
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Hello,
Thanks for your replying, your meaning is that the error was from the chemshell 3.6.0 software rather than charmm 42b2? Thank you again!


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