[O3A] proble aout QMD in open3dalign

[Ren X. <rx...@ho...>]

Hi:


I am trying to use QMD in open3dalign to generate the comformers of a compound, for further 3d-qsar research.


My system is: linux mint 18 64-bit, everything of the open3dalign was set properly.


My procedure are mainly.


1) open3dalign


2）import type=SDF file=test.sdf


3)

qmd prm_dir=/home/rxdcpu/00_Program/open3dtools/share/tinker \
keep_initial=NO \
minimizer=MINIMIZE \
min_maxiter=100 \
min_grad=0.001 \
rmsd=0.2 \
range=3.0 \
temperature=1000 \
runs=20 \
window=5 \
time_step=1.0 \
diel_const=1.0 \
gbsa=NO \
qmd_dir=qmd_dir \
remove_qmd_folder=NO

after I enter the above command, it seems the program began running. A terminal picture is as follow, no any error was found in log file (it's empty), and all of the cpu were in use.
[cid:247470ef-4e3c-44c9-bdc3-81a9951f14a4]

but there seems no much output file. the only output file 0001_000000.out is as follow.


     ######################################################################
   ##########################################################################
  ###                                                                      ###
 ###            TINKER  ---  Software Tools for Molecular Design            ###
 ##                                                                          ##
 ##                        Version 8.1  February 2017                        ##
 ##                                                                          ##
 ##               Copyright (c)  Jay William Ponder  1990-2017               ##
 ###                           All Rights Reserved                          ###
  ###                                                                      ###
   ##########################################################################
     ######################################################################


 Atoms with an Unusual Number of Attached Atoms :

 Type           Atom Name      Atom Type       Expected    Found

 Valence           1-CB           133              3         2
 Valence           2-CB           133              3         2
 Valence           3-CB           133              3         2
 Valence           4-CB           133              3         2
 Valence           5-CB           133              3         2

 Additional Partial Charges for Specific Atoms :

      Atom              Charge

         1              0.0000
         2              0.0000
         3              0.0000
         4              0.0000
         5              0.0000
         6              0.0284
         7              0.0366
         8             -0.0650
         9             -0.0650
        10              0.6300
        11             -0.1300
        12              0.5650
        13             -0.5000
        14             -0.5000

 Limited Memory BFGS Quasi-Newton Optimization :

 QN Iter     F Value      G RMS      F Move   X Move   Angle  FG Call  Comment

     0           NaN        NaN                                   1




Even after it run overnight, The program didn't complete. and no further output information came out.


Can any experienced user tell me what happened?



Best wishes

Xiaodong