Thanks for the tip. I implemented these steps by I'm still having the same
problem.
These are the computed energies for the first conformation, as given in file
_MMPBSA_complex_gb.mdout:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.0324E+14 2.5132E+13 1.7860E+15 HA2 1705
BOND = 2222.4107 ANGLE = 6085.2529 DIHED =
4574.8302
* VDWAALS = ************** EEL = -52263.5696 EGB =
-8681.4534
1-4 VDW = 2664.7813 1-4 EEL = 29817.0487 RESTRAINT =
0.0000
ESURF = 430.5994
I don't have this problem for the receptor (_MMPBSA_receptor_gb.mdout) or
ligand (_MMPBSA_ligand_gb.mdout)
*_MMPBSA_receptor_gb.mdout:*
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.6549E+04 1.9138E+01 1.1354E+02 CB 646
BOND = 1695.9831 ANGLE = 4668.8489 DIHED =
3514.6238
VDWAALS = -4709.0919 EEL = -37827.8824 EGB =
-7041.7999
1-4 VDW = 2033.8658 1-4 EEL = 20958.7822 RESTRAINT =
0.0000
ESURF = 157.9190
*_MMPBSA_ligand_gb.mdout:*
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -4.6648E+03 1.9499E+01 1.2670E+02 C 243
BOND = 526.4276 ANGLE = 1416.4040 DIHED =
1060.2064
VDWAALS = -1369.4285 EEL = -13851.2116 EGB =
-1983.2964
1-4 VDW = 630.9154 1-4 EEL = 8858.2665 RESTRAINT =
0.0000
ESURF = 46.9434
-Jose
On Mon, Nov 15, 2010 at 9:14 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
> Use the same input file you have here (after removing ntc=2) and use the
> MMPBSA.py command line as you normally would, except place the -make-mdins
> flag at the end of the command line. This will create all necessary mdin
> files that will be used during the calculation, without actually running
> the
> calculation. Then go into the newly created mdin files (named
> _MMPBSA_*.mdin) using your favorite text editor and add ntc=2 to the &cntrl
> section of those mdin files. Finally, use the same command from earlier to
> execute MMPBSA.py, except place the -use-mdins flag in place of the
> -make-mdins flag. This will tell MMPBSA.py to use mdin files that have
> already been created (and modified) as they are instead of having them made
> again by MMPBSA.py. Note, do not change the names of the respective mdin
> files because MMPBSA.py will only read in the mdin files with the names it
> has already assigned to them. This also gives a lot more flexibility to the
> user, but is also more prone to user errors that will not be caught by
> MMPBSA.py. So take caution when using these flags with MMPBSA.py,
>
> Good luck!
>
> -Bill
>
> On Mon, Nov 15, 2010 at 9:01 AM, Jose Borreguero <borreguero.gmail.com
> >wrote:
>
> > Dear Amber users,
> >
> > I'm having trouble using MMPBSA on a simulation that was carried out with
> > rigid bonds involving hydrogens. The Van der Waals computed energy by
> > MMPSBA
> > is out of scale. I though of including the 'ntc=2' option in the
> following
> > mmpbsa.in file:
> >
> > *&general
> > endframe=2525, verbose=1,
> > entropy=0,
> > ntc=2,
> > /
> > &gb
> > igb=2, saltcon=0.100
> > /
> > &pb
> > istrng=0.100, fillratio=2.0, scale=1.0
> > /*
> >
> > Unfortunately, the option 'ntc=3' is not understood by the parser. Does
> > anyone has an idea of how can I call for rigid bonds in MMPBSA ?
> >
> > Best regards,
> > Jose M. Borreguero
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 15 2010 - 08:00:03 PST
