In fact, in the command line I used $AMBERHOME/bin/MMPBSA.py, so it won't
go wrong. And in the output it clearly shows the MMPBSA.py executables
(mmpbsa_py_energy,cpptraj) are from AT12. And sander is from Amber11.
What else should I check please? Thanks!
Qiong
On Fri, May 18, 2012 at 2:35 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> If you type `which MMPBSA.py` does the MMPBSA.py executable from
> AmberTools12 appear correctly? And have you applied all bugfixes for
> AmberTools12?
>
> -Bill
>
> On Fri, May 18, 2012 at 2:29 PM, Qiong Zhang <qiong.zhang.qzh.gmail.com
> >wrote:
>
> > Dear Amber users,
> > I compiled the newest Ambertools12 under my home directory. And I need to
> > use Amber11 in another directory in the cluster. In order to use the
> Amber
> > executables from amber11/bin, but to use the AmberTools 12 executables
> from
> > amber12/bin, I followed the instructions by Jason on this page
> > http://jswails.wikidot.com/installing-ambertools-12-and-older-amber
> > export AMBERHOME=/home/user/amber12
> > export PATH=$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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri May 18 2012 - 12:00:04 PDT
