AMBER Archive (2005)

Subject: Re: AMBER: combine mdcrd using ptraj

From: Lihua Wang (lhw_at_broyde.nyu.edu)
Date: Thu Apr 07 2005 - 02:45:18 CDT

There is one approach that has always worked for me.

1. when you run ptraj, you output (using trajout) ONE frame in PDB format
with all WAT stripped.

2. load this output PDB file into xleap or tleap to generat the topology
file that you will use to view the trajectory. (you will also generate a
coordinate file but this will be of no use for this particular purpose.)

3. use this regenerated topology file to view your trajectory and it is
garranteed to work...

i have personally run into similar problems but they all turned out to be
my input problems instead of program bugs. Often times it is hard to
figure out what went wrong. Sometimes it is the differnece in numbering of
the atoms, sometimes it is the difference in atom names within your
original WAT-less topology file and ptraj-generated WAT-stripped
trajectory file. But the above approach makes sure that your
topology file matches exactly your trajectory because the topology file
was generated from a structure that is in turn generated by ptraj through
WAT stripping. And the trajectory file you are viewing is generated in
the same way by ptraj through WAT stripping.

This approach should work for any actions (and combinations of
them) on your trajectory (e.g. Na+ stripping, or residue stripping,
imaging...etc.) Just make sure that you do ptraj twice. In one, you
generate your desired trajectory. In the other, you generate ONE frame in
PDB.

E.g.
ptraj1.in
---------------------------------------------
trajin ../PfCo.md_1.mdcrd
trajin ../PfCo.md1.mdcrd
trajin ../PfCo.md2.mdcrd
trajin ../PfCo.md3.mdcrd
trajin ../PfCo.md4.mdcrd
trajin ../PfCo.md5.mdcrd
trajout PfCo_nowat.mdrcd nobox
rms first out PfCo.rmsfit @CA time 0.1
center :1-295
image familiar
strip :WAT
go
--------------------------------------------

ptraj2.in
--------------------------------------------
trajin ../PfCo.md_1.mdcrd 1 1 1
trajout pdbfortopology PDB
center :1-295
image familiar
strip :WAT
go
--------------------------------------------

Then you load your "pdbfortopology.1" (where .1 is added by ptraj as an
indication of the first frame) in tleap or xleap:

x=loadpdb pdbfortopology.1
saveamberparm x PfCo_nowat.top PfCo_nowat.crd

You should then be able to use this PfCo_nowat.top with PfCo_nowat.mdcrd
in viewing the trajectory.

hope that helps.

lihua

On Wed, 6 Apr 2005, xueping wrote:

> Date: Wed, 6 Apr 2005 23:59:54 -0700 (PDT)
> From: xueping <xueping22_at_yahoo.com>
> Reply-To: amber_at_scripps.edu
> To: amber_at_scripps.edu
> Subject: Re: AMBER: combine mdcrd using ptraj
>
> I tried before, not working...
>
> i try to process my mdcrd file one by one to strip out
> the water, it gives the same problem as well,
> something to do with striping out the water, but i am
> not sure why...
>
> The structure looks ok when i load mdcrd file with
> water one by one into the VMD, but i can't finish load
> all my mdcrd files, because this make my system
> freeze..
>
> Anyway, thanks for your suggestion.
>
> Regards
> xueping
>
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