Dear Daniel,
Thanks for your immediate reply. It worked with CPPTRAJ, where I used the
following script to do the job.
#########################################################
molsearch
parm ../parm.top
trajin ../md1.crd 1 2500 100
trajout md1.pdb pdb multi
#########################################################
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?
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?
Many thanks in advance
Regards
Anu
On Wed, Oct 16, 2013 at 8:40 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Try cpptraj; it will print TER cards in PDB files.
>
> -Dan
>
> On Wed, Oct 16, 2013 at 1:56 AM, anu chandra <anu80125.gmail.com> wrote:
> > Dear Amber users,
> >
> > I am working with trimeric protein. I am trying to generate snapshots
> every
> > 100th frame from simulation trajectories (mdcrd fromat) in PDB format
> with
> > the help of PTRAJ. Unfortunately, generated PDB lack TER card in between
> > the monomers. can anyone help to figure out this problem?
> >
> > Here is the script I used in PTRAJ.
> >
> > ###############################
> > trajin ../md1.crd 1 2500 100
> >
> > trajout md1.pdb pdb
> > ##############################
> >
> > Many thanks in advance.
> >
> > Regards
> > Anu
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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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>
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Received on Wed Oct 16 2013 - 22:30:02 PDT
