On Mon, Dec 10, 2012 at 7:35 PM, Chandrasekaran, Suryanarayanan <
s.chandrasekaran.jacobs-university.de> wrote:
>
>
> 12. prmtop file (Chandrasekaran, Suryanarayanan)
> 13. Re: prmtop file (Bill Miller III)
>
> Hi Bill Miller,
>
> Thank you for your reply, I dont find a specific command option for
> selecting a residue, i need to strip out water and do one by one, is there
> any specific command in Parmed.py to select the residue directly to write
> its property,
> I dont need the file only for visualization, i need to run MD using that
> .prmtop. if u have any tutorial on extracting residue will be more helpful.
>
What makes you think you need to strip water molecules out one-by-one? In
ParmEd, you can use the "strip" command to strip out an arbitrary mask
which you can easily use to delete all residues _except_ the one you're
interested in. Suppose the residue you're interested in is named "LIG" in
your prmtop, your prmtop name is "survas.prmtop" with a inpcrd/restart file
named "survas.inpcrd". The following command executed in a shell will run
parmed.py, giving you a stripped prmtop and inpcrd file ready for MD:
parmed.py survas.prmtop << EOF
loadRestrt survas.inpcrd
strip !:LIG
parmout lig.prmtop lig.inpcrd
EOF
Note, currently only parmed.py can write out an inpcrd file for you with
parmout or outparm (xparmed.py will only give you the option of writing a
prmtop, although this will change in the next AmberTools release). Also,
inpcrd files written by ParmEd will retain any velocity information present
in the original loaded restart.
However, ParmEd does not prevent anybody from doing "stupid" stuff. For
instance, if you strip out a residue in the middle of a protein chain and
write out a new prmtop, that system _will_ run in sander and pmemd without
warning, despite the fact that you have an unphysical system with dangling
bonds and a severed peptide chain. (ParmEd will, however, do *exactly*
what you tell it to do).
Where tleap uses something resembling chemical intuition to try to prevent
you from being foolish, ParmEd stays out of your way and does its best to
present you with a working prmtop that looks exactly the way you asked for
it.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Dec 11 2012 - 05:30:03 PST
