Hi,
Check out parmstrip in cpptraj. E.g. section 7.5.4 in AmberTools12 manual:
7.5.4. parmstrip
parmstrip <mask> [<parmindex>]
Strip atoms in <mask> from parm specified by <parmindex> (0, first parm
loaded by default).
Note that unlike the strip action, this permanently modifies the parm for
all subsequent
commands. This command can be used to e.g. quickly created stripped Amber
topology files:
parm mol.water.parm7
parmstrip :WAT
parmwrite out strip.mol.parm7
--Marc
On 3 June 2013 13:38, Paul Driscoll <pdrisco.nimr.mrc.ac.uk> wrote:
> Hi,
>
> I plan to strip down my trajectory files to protein backbone amide NH
> atoms only. How do I prepare a prmtop for use in subsequent ptraj
> analysis? [In other words how do I prepare a prmtop for only a subset of
> protein atoms?]
>
> Cheers,
> Paul
>
> --
> Paul Driscoll
> Group Leader
> Division of Molecular Structure
> MRC National Institute for Medical Research
> Tel. +44 (0)20 8816 2061 / +44 (0)7876 777937
> http://www.nimr.mrc.ac.uk/research/paul-driscoll
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>
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Received on Mon Jun 03 2013 - 06:00:04 PDT
