AMBER Archive (2008)

Subject: Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file

From: FyD (
Date: Wed Oct 29 2008 - 02:19:41 CDT

Quoting "David A. Case" <>:

> Thanks for your comments and problem reports. If the mol2 scheme
> doesn't work
> they way you need, please let us know -- I'd like to get rid of the prep and
> off formats, pushing everything to mol2, since that format is understood by
> lots of other programs. But if there are things mol2 can't do, we need to
> find that out, (and fix if possible).

I think a limitation of the mol2 file format is that it cannot contain
the connections (head & tail) between fragments + some information
defined using the LEaP 'set' command. This is why we load the mol2
files available in R.E.DD.B. in LEaP, add the head & tail for
fragments using a scripting approach, and save all in the OFF file

Another approach would be to create a new mol2 file format 'molx' that
would be displayable as the original .mol2 file format in LEaP, VMD
etc... but that would contain new cards defining the head and the tail
and more generally all the information stored in the OFF file format.
We started to code that in LEaP in the @<TRIPOS>MOLECULE section.

regards, Francois

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