Dear Amber users,
I compiled the newest Ambertools12 under my home directory. And I need to
use Amber11 in another directory in the cluster. In order to use the Amber
executables from amber11/bin, but to use the AmberTools 12 executables from
amber12/bin, I followed the instructions by Jason on this page
http://jswails.wikidot.com/installing-ambertools-12-and-older-amber
export AMBERHOME=/home/user/amber12
export PATH=$PATH:/home/user/amber12/bin:/home/user/amber11/bin
The input file is as follows:
&general
search_path=1,startframe=1, endframe=1, interval=1, verbose=2,
strip_mask=":Cl-", entropy=0, use_sander=0, netcdf=0,debug_printlevel=1
/
&gb
igb=2
/
&decomp
idecomp=1, print_res="1-2",dec_verbose=2
/
With search_path=1, the program did find the sander, but ended with a
sander error:
*CalcError: /lap/amber/11.0.17_AT1.5/bin/sander failed with prmtop
../prmtop2/9nd-35w.top*
And at the end of file _MMPBSA_complex_gb.mdout.0, it has:
Here is the input file:
File generated by MMPBSA.py
&cntrl
ncyc=0, cut=999.0, nsnb=99999, gbsa=2,
ntb=0, dec_verbose=2, imin=5,
idecomp=1, extdiel=80.0, igb=2,
surften=0.0072,
/
Residues considered as REC
RRES 2 36
END
Residues considered as LIG
LRES 1 1
END
Residues to print
RES 1 2
END
END
* error in reading namelist cntrl*
If I commented out the decomp part in the input file, it works fine. And
there is no problem if Amber11 and Ambertools1.5 under the same directory
were used.
Could you please suggest what might be wrong here? Thanks!
Qiong
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Received on Fri May 18 2012 - 11:30:03 PDT
