On Wed, Aug 22, 2012 at 9:33 AM, Francesco Pietra <chiendarret.gmail.com>wrote:
> Hi;
> I am using parm7 within NAMD. Is anything new with parm7 about
> carrying out equilibration of a protein in a water box? I mean, water
> model, flags? While range of temperatures have been explored, it seems
> that ff have been devised for 1 bar. Nonetheless, these are
> physiological conditions that would kill a deep water organism.
>
I'm confused... Is NAMD not running (and complaining about a badly
formatted topology file?). If it's 'running', then this is a question
about parameters and force fields, not so much the topology file...
If NAMD crashes, this is because NAMD does not adhere to the extensible
Amber prmtop format specification. I haven't tested the latest version of
NAMD, but NAMD 2.8 will not run with AmberTools12-generated topology file
because a couple extra flags were added to the prmtop, but they can be
deleted without much effort. The flags that are safe to delete (for use
with NAMD only!) are ATOMIC_NUMBER, SCEE_SCALE_FACTOR, SCNB_SCALE_FACTOR,
and IPOL.
ParmEd can do this within its scripting environment, so a script that looks
like this:
!amber_prmtop.deleteFlag('ATOMIC_NUMBER')
!amber_prmtop.deleteFlag('SCEE_SCALE_FACTOR')
!amber_prmtop.deleteFlag('SCNB_SCALE_FACTOR')
!amber_prmtop.deleteFlag('IPOL')
outparm new_prmtop.parm7
You will need to use the "-e" flag to allow python commands in ParmEd to
use the above commands, though (note, ! is needed to activate the python
interpreter for that command).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Aug 22 2012 - 07:30:02 PDT
