On Thu, Oct 17, 2013 at 11:34 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
Hi,
Thanks for the reply.
> Hi,
>
> On Wed, Oct 16, 2013 at 11:19 PM, anu chandra <anu80125.gmail.com> wrote:
> > molsearch
>
> FYI in cpptraj V13 the 'molsearch' keyword is no longer needed
> (molecules are always searched for) and is in fact deprecated.
>
If I use the CPPTRAJ script without 'molsearch' keyword, the generated PDB
files lack the TER cards in between. Here is the script I used
#########################################################
parm ../parm.top
trajin ../md1.crd 1 2500 100
trajout md1.pdb pdb multi
#########################################################
Regards
Anu
> > 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,...so on), instead of numbering with
> exact
> > frame number ( ie. filename.frame1, filename.frame101,
> > filename.frame201,...so 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.
>
> -Dan
>
> --
> -------------------------
> 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) 585-6208 (Fax)
>
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Received on Thu Oct 17 2013 - 21:30:03 PDT
