Re: AMBER: ptraj problem

From: Thomas E. Cheatham, III <>
Date: Thu, 1 Sep 2005 14:54:24 -0600 (Mountain Daylight Time)

> When I used ptraj to get bfactors from my trajectory file, the
> rms first out zb.b :1-298.CA
> atomicfluct out bfactor.out .CA byatom bfactor
> the calculation can be done smoothly, however, I noticed that there is
> only more than 70 B-factors, which should be 298, in the bfactor.out

Why do you think there should be 298 CA atoms? ptraj/rdparm is
recognizing the atom selection ".CA" as listed (a subset is below)

> :1.CA,:6.CA,:10.CA,:16.CA,:17.CA,:21,CA,:22.CA,:26.CA,:31,CA,:32.CA

This suggests that residues 2-5 do not contain an atom named CA. If ptraj
is not matching correctly, i.e. residues 2-5 *do* indeed each contain an
atom named CA, then please let me know and send me the prmtop file so I
can figure out why they are not matched. You can see what the prmtop has
by reading it in via rdparm and using the atoms command

   atoms .CA

you can also use the "checkmask" command in rdparm to show what ptraj is
selecting for a given mask choice.

(you can also see what atoms are present by creating a PDB file and
looking at this by hand).

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
/-\ (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A

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Received on Thu Sep 01 2005 - 22:53:03 PDT
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