If you type `which MMPBSA.py` does the MMPBSA.py executable from
AmberTools12 appear correctly? And have you applied all bugfixes for
AmberTools12?
-Bill
On Fri, May 18, 2012 at 2:29 PM, Qiong Zhang <qiong.zhang.qzh.gmail.com>wrote:
> 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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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri May 18 2012 - 12:00:03 PDT
