AMBER Archive (2005)

Subject: AMBER: combine mdcrd using ptraj

From: xueping (xueping22_at_yahoo.com)
Date: Wed Apr 06 2005 - 23:41:48 CDT

Dear all,

I use ptraj to combine my mdcrd files, below is my
script:

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

Then, i load the PfCo_nowat.mdrcd file to VMD, and
choose type:crdbox after loading my prmtop file
without water. The structure loaded look so weird, it
has alot of long lines and it doesn't look ok....

So, i check my mdcrd file one by one, loading it in
VMD with the prmtop file with water, and it look ok
for all the mdcrd files...

Is it because of my ptraj script? It is same to my
average structure that i produce using ptraj, the
structure look so weird. Please give me some
suggestions. Thank you very much.

Regards
xueping

                
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