On Tue, Jan 15, 2013 at 11:01 AM, Andrew Anighoro <
andrew.anighoro.unimore.it> wrote:
> Dear all,
> I am using amber12 with the ff12SB force field. I would like to
> post-process MD trajectories
> (for binding energy calculations) using mm_pbsa, but it seems that the
> newer atom types of the ff12SB force field have not been incorporated
> into
> pbsa (PB Bomb in pb_aaradi(): No radius assigned for atom....etc etc).
> I have seen plenty of discussion about this issue in the amber mailing
> list.
> Unfortunately, editing the topology files with xparmed when huge
> numbers of mm_pbsa runs are planned is not such a straightforward
> solution....
>
parmed.py is a text-based version of ParmEd that is easily scriptable (at
least in my opinion). So something like this
#!/bin/sh
# The first argument to this script is the prmtop
new_parm=`basename $1`_mod.prmtop
parmed.py $1 << EOF
change AMBER_ATOM_TYPE .%X1 Y1
change AMBER_ATOM_TYPE .%X2 Y2
outparm $new_parm
EOF
program -p $new_parm ...
therefore may I ask if there is anybody so kind to provide some basic
> instructions on where to define such atom types in the pbsa source
> code.
> I think that would be of great help.
> Thank you very much in advance for your help.
>
If you grep for pb_aradii in the pbsa source code
($AMBERHOME/AmberTools/src/pbsa), you should see where that subroutine is
called and where it is defined. You can add the parameters inside the
pb_aradii subroutine.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jan 15 2013 - 09:00:04 PST
