AMBER Archive (2008)

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

From: Wei Zhang (zweig_at_scripps.edu)
Date: Mon May 12 2008 - 09:34:40 CDT

Hi,

     You can try to save it as mol2 format and use sleap to read it.

     Please let me know if you have any problem.

     Sincerely,

     Wei

On May 11, 2008, at 8:36 AM, WANG,YING wrote:

> Thanks a lot!
>
>
>
> On Sat May 10 11:24:41 EDT 2008, "David A. Case" <case_at_scripps.edu>
> wrote:
>
>> 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
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
>
> --
> WANG,YING
> Mechanical and Aerospace Engineering
> University of Florida
> Office: NEB 139
> TEL: 001-352-846-3030
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu