Hi,
Sorry for taking so long to reply but. I sent the files directly to you
via dropbox.
The command that I used to run mmpbsa.py is:
$AMBERHOME/bin/MMPBSA.py -O -i mm-pbsa.in -cp com_wt.top -rp
recCFH_wt.top -lp ligB_wt.top -y 2frames.mdcrd -mc 2Bmut_comp.top -ml
2Bmut_lig.top -mr recCFH_wt.top&
And the mm-pbsa.in is
sample input file for running alanine scanning
&general
startframe=1, endframe=2, interval=1,
verbose=1,
ligand_mask=':1-200,806,810',
receptor_mask=':201-805,807-809,811-813',
/
&pb
inp=1, radiopt=0, exdi=80, indi=3.0,
cavity_surften=0.00542, cavity_offset=-1.008,
fillratio=4, scale=2.0, linit=1000, istrng=0.100,
/
&alanine_scanning
/
Thank you very much,
Alexandra
Em 2014-02-24 14:57, Jason Swails escreveu:
> On Mon, 2014-02-24 at 14:28 +0000, almarques wrote:
>> Thank you. I did that but I obtained the same error.
>> I also extracted the pdb file from frame 1 of the trajectory without
>> solvent to see if the residue numbers are correct and indeed they
>> match
>> those in the top file of the complex. Does anyone has other
>> suggestion
>> about what may be wrong?
>> I am using AmberTools12.
>
> Try AmberTools 13 instead. If you send me your topology files and an
> example with your topology files and a trajectory that has 2 frames I
> will look into it (in a compressed tarball please). You may have to
> post them on Dropbox or something if they're too big to attach here.
>
> Thanks,
> Jason
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Received on Wed Feb 26 2014 - 14:30:03 PST
