Thanks for the comments, guys.
First, I should explain I am working from Amber11 and did not know about
cpptraj (will try to obtain it now) and second, I am after keeping N-H
_bond_ atoms, i.e. two atoms per residue (for time correlation and IRED
analysis). I understand Jason's caution. I'll try what he suggests and
see if applying the mask in that can get me around my memory limitation
problems.
Cheers,
Paul
On 03/06/2013 14:18, Jason Swails wrote:
> On Mon, Jun 3, 2013 at 8:38 AM, 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?]
>>
> As Marc suggested, parmstrip will do the trick (ParmEd also has a stripping
> ability, but if you're already stripping a mask with cpptraj you might as
> well use cpptraj to strip the topology, too).
>
> I think it's even easier than that, though. In cpptraj, do your
> stripping like this:
>
> parm my.parm7
> trajin mytraj.nc
>
> strip !:N outprefix backbone_amide
>
> trajout backbone_amide.nc
>
> This will create a trajectory file 'backbone_amide.nc' and a matching
> topology file backbone_amide.my.parm7.
>
> However, I would be wary of stripping the coordinates down to _just_ a
> single atom in each residue, since some actions in cpptraj make use of bond
> information. If it was me, I would just strip out the solvent and leave
> the entire solute intact and do any analyses you have using a specific atom
> mask.
>
> HTH,
> Jason
>
--
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 03 2013 - 07:00:02 PDT
