AMBER Archive (2008)

Subject: Re: AMBER: cannot read big .pdb files

From: Lynn F. Ten Eyck (
Date: Sat May 10 2008 - 11:37:02 CDT

This restriction is due to the definition of the PDB format and not
due to anything specific to AMBER. The field width for each
coordinate is limited to eight characters, including the sign (only
required if negative). If your coordinates cannot be specified to
sufficient precision within that limit, you will have to find another
data representation than standard PDB format (and, of course, a
program that can read/write it).

The PDB standard has been around for thirty years, and is showing its
age. This is why the PDB does not maintain its data internally in
this format, but uses mmCIF. Unfortunately during this thirty years
there has been a truly huge investment in software that reads and
writes this standard. Any changes to it will break a LOT of software,
much of which is very difficult to update, and of course introduces
all of the ancillary problems of updating the software and updating
data files all over the world.

Best regards,
Lynn Ten Eyck

On 9 May 2008, at 19:00, WANG,YING wrote:

> Hi, Dear AMBERS,
> I build a huge system and express it by .pdb file. But the space
> between x,y,z parameters are limited. So if my system is too large
> then I can not let it read by amber. For example,
> ATOM 4112 xx xxx 197 -0.209 -2.116-999.344
> ATOM 4113 xxx xxx 197 0.167 -1.985********
> ATOM 4114 xx xxx 197 -0.201 -1.486-997.016
> ATOM 4115 xx xxx 197 -1.166 -1.651-997.047
> ATOM 4116 xx xxx 197 0.472 -2.629-996.483
> ATOM 4117 xxx xxx 197 0.135 -2.888-995.623
> ATOM 4118 xx xxx 197 0.611 0.635********
> ATOM 4119 xx xxx 198 -0.108 0.357********
> Could anybody tell me how to deal with it? Thanks a lot!!
> --
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

Lynn F. Ten Eyck Office: 3131 Atkinson Hal
UCSD /MC 0505 Tel: +858.534.5141
San Diego Supercomputer Center Fax: +858.822.3610
9500 Gilman Drive
La Jolla, CA 92093-0444

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to