Re: bond length in terminal patches

From: Peter Freddolino (
Date: Sat Nov 22 2008 - 20:33:38 CST

Hi Vlad,
normally psfgen (the backend used by autopsf) guesses the coordinates of
missing atoms based on entries in the topology file. However, if there
isn't enough information, it uses a default bond angle and distance,
which is where the 1 A bonds come from. This shouldn't be a problem so
long as you minimize and equilibrate your system sanely, since the bonds
will very quickly go to their equilibrium lengths.

CHINDEA Vlad wrote:
> Hi everybody
> I have encountered the following situation: the bond length of the
> atoms added as terminal patches (NTER, CTER) by AutoPSF on a few
> molecules that I have worked on is allways 1,00 A while I would have
> expected for example a bond length of 0,98 A for H-N bond or about
> 1,43 A for C-O bond and 1,23 A respectively for a C=O bond in the CTER.
> My question is the following: Is this 1,00 A bond length correct and
> is the program behaving as it should when doing this ? Or is there a
> problem with my installation, system etc.?
> Many thanks and kind regads
> Vlad
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