AMBER Archive (2008)

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

From: WANG,YING (wangying_at_ufl.edu)
Date: Mon May 12 2008 - 14:42:27 CDT

HI,
Do anybody know how to convert .xyz to .mol2 format?

Thanks a lot!!

Ying

On Mon May 12 10:34:40 EDT 2008, Wei Zhang <zweig_at_scripps.edu>
wrote:

> 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
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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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>>
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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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