[AMBER] How to setup QM/MM-GBSA calculation ?

From: mish <smncbr.gmail.com>
Date: Mon, 3 Jan 2011 18:35:21 +0100

Dear Amber Users,

I would like to ask about the way to do QM/MMPB(GB)SA calculation in AMBER.
When we run the normal MMPB(GB)SA calculation using perl script, it
generates three intermediate files during execution sander_com.in,
sander_rec.in, sander_lig.in which are used by sander for further
calculation. If i understand well, in QM/MMPB(GB)SA calculation we have to
insert QM keywords in these files. can mm_pbsa.pl script post process that
output of QM/MM calculation ?

if yes then, Is there any way to input QM keywords through the
mmpbsa.inscript ? or we have to change the generated
sander_com.in, sander_rec.in, sander_lig.in during execution ?

or if script can not post process the output of QM/MM calculation then, i
cam generate the snapshots followed by -

1- make a loop over all snapshots of the complex and run the calculation in
sander using by using QM/MMGBSA input file (previously posted by Markus),


 ntf = 1, ntb = 0,
 igb = 5, dielc = 1.0,
 cut = 1000.0, nsnb = 10,
 scnb = 2.0, scee = 1.2,
 intdiel= 1.0, extdiel=80.0,
 rgbmax = 1000.0, gbsa = 0,
 qmmask=".11092-11095,12467-12549" ! (QM region)
 qmcharge=0, !(Charge on QM region)
 qm_theory="DFTB", !(Use the DFTB semi-empirical Hamiltonian)
 qmcut=1000.0, !(Use1000 angstrom cut off for QM region)
 printcharges=1, !print QM charges
 dftb_telec=100.0 !temperature for fermi func.

2- Process QM/MM output file from sander and write the Energy part in
snap_com.all.out, (what about surface area ? )

3- Repeat the step 1 & 2 for receptor as well as ligand.

Can any of you dictate how to do the post processing ? How to get delta G
from those files ?

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Received on Mon Jan 03 2011 - 10:00:02 PST
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