Thanks a lot!
erm, Could AMBER read other format data?
On Sat May 10 12:37:02 EDT 2008, "Lynn F. Ten Eyck"
<Lynn.TenEyck.ucd.ie> wrote:
> 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!!
>>
>>
>>
>>
>> --
>> WANG,YING
>>
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>
> 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
>
> -----------------------------------------------------------------------
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>
>
--
WANG,YING
Mechanical and Aerospace Engineering
University of Florida
Office: NEB 139
TEL: 001-352-846-3030
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Received on Wed May 14 2008 - 06:07:07 PDT
