Re: AMBER: PTRAJ $ Antechamber

From: David A. Case <>
Date: Sat, 12 Mar 2005 14:17:49 -0800

On Thu, Mar 10, 2005, Andrew Box wrote:

> The problem is that the pdb files that were generated had no charge
> information....,

PDB-format files are not supposed to have any charge information in them,
that is, there is no field that is designed for molecular charges.

There are some unofficial extensions to the standard (so-called "pqr" files)
that mostly look like PDB files, but have charges. Or there are formats
like "mol2" or the (Amber-specific) "off" files that are desitned to hold

So, the key question is: what are you going to do with the file you are trying
to create? If the downstream program knows about the pqr format, that might
be the easiest way to go, using ambpdb (for example) to create the pqr file.


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Received on Sat Mar 12 2005 - 22:53:00 PST
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