On Thu, Oct 15, 2015 at 10:21 AM, Sun <sunbintyy.163.com> wrote:
> Hi Jason,
> Thanks for your help. The modified Test.pdb worked well and the number of
> atoms in the xyz file now is the same
> as that in the pdb file. However, Step 3 still did not work, the prmtop
> and inpcrd files were still empty.
>
> Also I tried to execute the Step 3 interactively and at the end an error
> message appeared saying there was some trouble on opening the key_file.
> -------------------------------------------------------------
> [username.host]$ tinker_to_amber
> analoutfile:
> Test.analout
> xyz_file:
> Test.xyz
> pdb_file:
> Test.pdb
> title:
> Amoeba Fore Field
> prmtopfile (output):
> Test.prmtop
> inpcrd_file (output):
> Test.inpcrd
> trouble opening key_file
> --------------------------------------------
>
> But the content of the key_file is "parameters
> /home/username/apps/tinker/params/amoebapro13" ( /home/username/apps/tinker
> is $TINKER_HOME) and also in step 1 the key_file could be open without any
> problem.
> So could give me any help about what happened ?
>
Maybe it's not trying to open the file named "key_file"? This is the part
of the code that prints that error:
open(unit=key_unit,file=key_file,status='old',iostat=ios)
if ( ios /= 0 )then
write(6,*)'trouble opening key_file ',key_file
stop
endif
So tinker_to_amber is getting stuck at *opening* the file. The only thing
this could mean is that either the file it is trying to open does not
exist, or it does not have read permissions for the owner of the running
process. I would suggest focusing your efforts to fix this problem on
those possibilities.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 15 2015 - 08:00:03 PDT
