On Wed, 2014-02-26 at 22:13 +0000, almarques wrote:
> 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
> /
I cannot reproduce your error using AmberTools 13. I get a bunch of
error/warnings along the lines of:
Error: Atom 12403 was assigned a lower molecule # than previous atom. This can
Error: happen if 1) bond information is incorrect or missing, or 2) if the
Error: atom numbering in molecules is not sequential. If topology did not
Error: originally contain bond info, 1) can potentially be fixed by
Error: increasing the bondsearch cutoff offset (currently 0.200). 2) can be
Error: fixed by either using the 'fixatomorder' command, or using
Error: the 'setMolecules' command in parmed.py.
Error: Could not determine molecule information for com_wt.top.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for com_wt.top.
This error has been described elsewhere, but for MMPBSA.py should not be
an issue. Please make sure you are using the latest version of
AmberTools 13 for this calculation.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 27 2014 - 10:00:03 PST
