AMBER Archive (2005)

Subject: Re: AMBER: ptraj problem

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Thu Sep 01 2005 - 15:54:24 CDT


> When I used ptraj to get bfactors from my trajectory file, the ptraj.in
...
> rms first out zb.b :1-298_at_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_at_CA,:6_at_CA,:10_at_CA,:16_at_CA,:17_at_CA,:21,CA,:22_at_CA,:26_at_CA,:31,CA,:32_at_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
-/-
/-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A http://www.chpc.utah.edu/~cheatham

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu