Re: [O3A] proble aout QMD in open3dalign

[Paolo T. <pao...@un...>]

Hi Ren,

can you share test.sdf with me? You don't need to reply to the list - 
just reply to me.

Regards,
Paolo

On 06/06/17 19:29, Ren Xiaodong wrote:
>
> 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.
>
> 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
>