Re: [AMBER] PTRAJ - Problem with inserting TER card

From: Daniel Roe <>
Date: Thu, 17 Oct 2013 12:04:33 -0600


On Wed, Oct 16, 2013 at 11:19 PM, anu chandra <> wrote:
> molsearch

FYI in cpptraj V13 the 'molsearch' keyword is no longer needed
(molecules are always searched for) and is in fact deprecated.

> But, the genereated PDB files are named with the format ' filename.frame#
> ', where the frame numbers are in sequential order ( ie. filename.frame1,
> filename.frame2, filename.frame3, on), instead of numbering with exact
> frame number ( ie. filename.frame1, filename.frame101,
> filename.frame201, on). I would like to keep the exact frame number
> and is it possible to do while generating the PDB files?

Unfortunately no. This is done to maintain backwards compatibility
with ptraj. The primary reason is so that the frame numbers of the
filenames match up with the frame #s of any generated data (from e.g.
rms, distance, etc).

> Moreover, since I am working with a trimeric protein, I would like to add
> three different chain ID after each 'TER' card. But, the ' chain <ID> '
> option with ' trajout' command will hold only single character. Is there
> a way to add three different chain IDs to the PDB files?

Also no, sorry. The 'chainid' keyword is really just a hack for single
molecules; cpptraj currently doesn't handle things like chain ID or
original frame #s in PDB files, although this support is currently
under development.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Oct 17 2013 - 11:30:03 PDT
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