[gmx-users] web lab viewer

John Kerrigan kerrigje at UMDNJ.EDU
Thu Jan 23 20:30:13 CET 2003

From: David <spoel at xray.bmc.uu.se>
To: gmx-users at gromacs.org
Date: 23 Jan 2003 19:10:41 +0100
Reply-To: gmx-users at gromacs.org

On Fri, 2003-01-24 at 05:55, sadhna wrote:
> hi,
>    I mean that for other carbonyl bonds it shows two lines for double
> bonds but for my residue it shows one line and when i go to the add
> hydrogen menu the hydrogen gets added to the corbonyl oxygen also which it
> should not!! It doesn't add hydrogen to the carbonyl oxygen for other
> residues.
the program (web lab viewer) is less intelligent than you think. The
bond is probably a fraction too short. Measure it after em and check
whether it is correct. If not go back to your topology...
> rgds
> sadhna

Might I add that Web Lab Viewer or ViewerPro is a "refined" molecule viewer.
That is to say, it's intelligence is limited to refined file formats like
Tripos mol2 and MDL mol files.  Anything goes with pdb files (if that is the
format you are porting).  Web Lab viewer takes its best guess and often
guesses incorrectly.  Do not rely on Web Lab viewer to correct your
structures.  Rather, use Web Lab viewer as a tool to make fine adjustments
to your structure for viewing purposes.  Minimize your structure beforehand
using Gromacs as David suggests; however, realize that Web Lab Viewer may
still get it wrong after minimization and you may still need to make fine
adjustments (typically formal charges, atom types, etc.) for display.



John E. Kerrigan, Ph.D.
Computational Biologist

Adjunct Associate Professor
Dept. of Pharmacology

Academic Computing Services
RWJMS-Univ. of Medicine and Dentistry of NJ
675 Hoes Lane
Piscataway, NJ 08854

(732) 235-4473  phone
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