Hi,
Unfortunately you currently can't combine different
trajectories/topologies into a single run in cpptraj; each 'trajin' is
run in succession. The only way I can think of approaching this
problem is to manually combine the trajectories and topologies
yourself (maybe using PDB intermediates?) and do it as a single
trajin, adjusting your mask appropriately, e.g.:
parm combined.prmtop
trajin combined.mdcrd
distance Pclamp :16.CA :N.CA
where N is (158+Nres1).
-Dan
On Fri, Feb 1, 2013 at 8:11 AM, HM <scienceamber.gmail.com> wrote:
> Hi All,
> I was using below mentioned lines to calculate the distance between two
> atoms from two different simulations.
>
>
> parm complex1.prmtop
> parm complex2.prmtop
> trajin ../nowat12ns.mdcrd parm complex1.prmtop
> trajin PfActin_prime/nowat12ns_atp.mdcrd parm complex2.prmtop
>
> distance Pclamp :16.CA :158.CA out Pclamp_PfNoLat.dat
>
> Can anyone correct me how to modify last distance line so that i can get
> the distance measurement between two atoms from two the trajectories.
>
> Thanks,
> HM
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Feb 01 2013 - 08:00:03 PST
