[gmx-users] specbond recognised but not built

Grange Hermitage ghermitage at y7mail.com
Sun Jun 29 14:41:37 CEST 2008

Thankyou very much Tsjerk, indeed this was the problem. I am most relieved this was the solution.
I had assumed the distance was an upper bound on the acceptable distance.

----- Original Message ----
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, 29 June, 2008 5:50:22 PM
Subject: Re: [gmx-users] specbond recognised but not built

Hi Grange,

It recognizes the possibility of having a bond between these atoms.
That's where the distance matrix comes in. But if a bond were made,
you'd have a statement right after the distance matrix saying
something like "linking atom ... and atom ...". It doesn't happen, and
the reason is the following (you might want to search "specbond" in
the user list archives): You have set your distance at 0.2 nm. pdb2gmx
checks whether the actual distance is within 10% of the distance
specified. The actual distance is 0.134, which lies well under the
target distance. Therefore it doesn't make the bond. Try to set the
bond length in specbond.dat between 0.13 and 0.14..

Hope it helps,

      Get the name you always wanted with the new y7mail email address.
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