Hi,
This "flat" PDB makes me think that maybe one (or more) of your
coordinate columns may be getting "overloaded" - PDB is a fixed format
and so is susceptible to such things. Can you try writing out a single
frame as a mol2 file (which is not as fragile as the PDB format) and
see if that looks better? Input:
parm gagIT.prmtop
trajin gagIT_md950ns.mdcrd 1 1
trajout gagIT_md950ns.mol2
Thanks,
-Dan
On Wed, Mar 18, 2015 at 9:40 PM, Chinh Su Tran To
<chinh.sutranto.gmail.com> wrote:
> Dear Amber users,
>
> I used cpptraj to convert a trajectory frame into pdb format, but I got
> very "weird" pdb file (Sorry, I cannot attach it here as it is more than
> 5Mb and the post was bounced back). When I visualized it, it gave me a
> "flat" structure with clashes (image attached).
> Could you please help comment if I missed something? Thanks.
>
>> parm gagIT.prmtop
> Reading 'gagIT.prmtop' as Amber Topology
>> trajin gagIT_md950ns.mdcrd
> Reading 'gagIT_md950ns.mdcrd' as Amber Trajectory
>> trajout gagIT_md950ns.pdb pdb parm gagIT.prmtop onlyframes 2500
> Writing 'gagIT_md950ns.pdb' as PDB
> Saving frames 2500
>> run
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES:
> 0: 'gagIT.prmtop', 59573 atoms, 17761 res, box: Trunc. Oct., 17262 mol,
> 17248 solvent, 2500 frames
>
> INPUT TRAJECTORIES:
> 0: 'gagIT_md950ns.mdcrd' is an AMBER trajectory, Parm gagIT.prmtop (Trunc.
> Oct. box) (reading 2500 of 2500)
> Coordinate processing will occur on 2500 frames.
>
> OUTPUT TRAJECTORIES:
> 'gagIT_md950ns.pdb' is a PDB file, Parm gagIT.prmtop: Writing frames 2500
> TIME: Run Initialization took 0.0001 seconds.
>
> BEGIN TRAJECTORY PROCESSING:
> ----- gagIT_md950ns.mdcrd (1-2500, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 2500 frames and processed 2500 frames.
> TIME: Trajectory processing: 49.1169 s
> TIME: Avg. throughput= 50.8989 frames / second.
>
> ACTION OUTPUT:
> ---------- RUN END ---------------------------------------------------
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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 Mar 19 2015 - 21:30:02 PDT
