Re: AMBER: ptraj: calculating distances between atoms in charges residues

From: Thomas Cheatham <>
Date: Fri, 26 May 2006 10:12:40 -0600 (Mountain Standard Time)

> I am trying to calculate the distance between the atoms in all charged
> residues in AMBER8, and I have read on the reflector site that it should be
> possible to calculate distances between heavy atoms in the hbond mode if the
> acceptor atoms are specified twise, but it don't work in my case. Do anyone
> have any idea why it dosen't work? see my script below.

There are two ways to calculate distances, explicitly with the distance
command and indirectly via the hbond command.

> # specify the electron pair DONOR
> donor mask :ASP.OD1
> donor mask :ASP.OD2
> donor mask :GLU.OE1
> donor mask :GLU.OE2
> #-- Acceptors from standard amino acids
> acceptor mask :ARG.NH1 :ARG.NH1
> acceptor mask :ARG.NH2 :ARG.NH2
> acceptor mask :ARG.NE :ARG.NE
> acceptor mask :LYS.NZ :LYS.NZ

As these selections are chosen, information should be printed. To see if
the selections are as you expect, set prnlev 3 prior to the selection and
check the list of selections to make sure they make sense.

> hbond distance 6.0 angle 0.0 out ion-contact.txt

This should work, however it doesn't produce much useful output. To get
more useful output, add the "series" keyword and see if this then provides
the information you needed...

hbond series h1 distance 6.0 angle -1.0 out ion-contact.txt

Note that the above will only investigate the salt bridges you specified
(not ion-contact); to add in ions (assuming the names are K+)

hbond series h1 distance 6.0 angle -1.0 out ion-contact.txt \
   solventdonor K+ K+ \
   solventacceptor K+ K+ K+

\-/ 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 Fri May 26 2006 - 21:05:27 PDT
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