[AMBER] Sander 01_Min.out error

From: <leifepeterson.sbcglobal.net>
Date: Sat, 15 Sep 2018 21:23:44 -0500

When trying the Alanine leap example, after copying the leap outputs and
other files into the binary folder /amber18/bin (this is just temporary to
test sander), and using the following command:

 

./sander -O -i 01_Min.in -o 01_Min.out -p prmtop -c inpcrd -r 01_Min.rst
-inf 01_Min.mdinfo

 

I get an output for 01_Min.out which looks like:

 

 

          -------------------------------------------------------

          Amber 18 SANDER 2018

          -------------------------------------------------------

 

| Run on 09/15/2018 at 21:05:48

 

| Executable path: ./sander

| Working directory: /home/lep/amber18/bin

| Hostname: Unknown

  [-O]verwriting output

 

File Assignments:

| MDIN: 01_Min.in


| MDOUT: 01_Min.out


|INPCRD: inpcrd


| PARM: prmtop


|RESTRT: 01_Min.rst


| REFC: refc


| MDVEL: mdvel


| MDFRC: mdfrc


| MDEN: mden


| MDCRD: mdcrd


|MDINFO: 01_Min.mdinfo


| MTMD: mtmd


|INPDIP: inpdip


|RSTDIP: rstdip


|INPTRA: inptraj


 

 

Here is the input file:

 

Minimize


 &cntrl


  imin=1,


  ntx=1,


  irest=0,


  maxcyc=2000,


  ncyc=1000,


  ntpr=100,


  ntwx=0,


  cut=8.0,


 /


 

---------------------------------------------------------------------------- 
----
   1.  RESOURCE   USE: 
----------------------------------------------------------------------------
----
 
| Flags:
 getting new box info from bottom of inpcrd
|  INFO: Old style inpcrd file read
 
| peek_ewald_inpcrd: Box info not found in inpcrd
 
 
FYI - the contents of inpcrd are:
 
ACE
    22
   2.0000010   1.0000000  -0.0000013   2.0000010   2.0900000   0.0000001
   1.4862640   2.4538490   0.8898240   1.4862590   2.4538520  -0.8898200
   3.4274200   2.6407950  -0.0000030   4.3905800   1.8774060  -0.0000066
   3.5553754   3.9696488  -0.0000031   2.7331200   4.5561601  -0.0000013
   4.8532621   4.6139253  -0.0000043   5.4075960   4.3155388   0.8898152
   5.6613044   4.2208425  -1.2321480   5.1232615   4.5213630  -2.1312016
   6.6304840   4.7189354  -1.2057907   5.8085401   3.1408724  -1.2413850
   4.7126759   6.1294185   0.0000014   3.6006445   6.6527027   0.0000062
   5.8460533   6.8348833   0.0000025   6.7370014   6.3591620  -0.0000004
   5.8460551   8.2838837   0.0000062   4.8185761   8.6477349   0.0000104
   6.3597984   8.6477313   0.8898283   6.3597900   8.6477354  -0.8898187
 
 
 
 
 
 
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Received on Sat Sep 15 2018 - 19:30:02 PDT
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