Re: [AMBER] Best practice for charmm to AMBER conversion with HEME group

From: David A Case <>
Date: Sat, 8 Oct 2016 20:45:46 -0400

On Fri, Oct 07, 2016, Korey M Reid wrote:

> CharmmWarning: Detected PSF molecule section that is WRONG. Resetting molecularity.
> MissingDisulfide: Detected two cysteine residues whose sulfur atoms are within 3
> Angstroms. Rename CYS to CYX in the PDB file and use the
> 'bond' command in tleap to create the disulfide bond
> These warnings I am not competent yet to investigate and the last
> confuses me to no end seeing that the closes 2 cystines (and only
> cystines) are at least 27Ang apart....

How did you determine that the two cysteines are 27 Ang apart? Did you look
at the Amber coordinates (not the CHARMM ones you started from)? Have you
visualized the system on the Amber side?

Also, check the box sizes on the Amber side: a bad set of box parameters could
lead to distances that are much shorter than you think, becuase the distance
is being calculated to a molecule in a neighboring unit cell.

Of course, this doesn't say how to fix anything, but it might provide some
clues about what is happening.


AMBER mailing list
Received on Sat Oct 08 2016 - 18:00:02 PDT
Custom Search