AMBER Archive (2008)

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

From: David A. Case (case_at_scripps.edu)
Date: Sat May 10 2008 - 10:24:41 CDT

On Fri, May 09, 2008, WANG,YING wrote:

> 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********

You can write the coordinates with less precision, if you want to use
the pdb format. For example, instead of -1001.325 (which won't fit into 8
columns), use -1001.32.

There may be other solutions people can come up with.

...good luck...dac

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