[gmx-users] .pqr to .pdb

[mohsen ramezanpour]

On Thu, Dec 2, 2010 at 5:58 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> mohsen ramezanpour wrote:
>
>> Dear Tsjerk
>>
>> some information exist in pdb file which are not peresent in pqr and vise
>> versa.
>> I want to convert them to eachother in a way to conclude one's information
>> to the other file.
>> as you know a typical pdb file has a definite colomns and each of them
>> present a definite charachter(for example charge,X-coordinate,...)
>>
>
> Charges are not typically in .pdb files, and they certainly don't precede
> the x-coordinate.

Ok.I agree with you

>
>
>  my pqr has more atoms than original pdb,but It dosen't have any
>> coordinates.
>>
>
> Then it sounds like you have a useless .pqr file.  The format of a proper
> .pqr file is identical to that of a .pdb file, except that in place of
> B-factor and occupancy fields, the charge and radius are given.  Thus, what
> Tsjerk told you should work, but perhaps you have a mangled input file that
> makes this impossible.
>

Ok.I will try to produce another .pqr file again.I think both are you are
right ,it seems to me my file is useless.
Thanks

>
> -Justin
>
>  besides converting as you said dosen't solve the problem,because PYMOL can
>> not read this converted file.it <http://file.it> needs a file who has
>> included atoms coordinates
>>
>>
>> thanks in advance for your reply
>> Mohsen
>>
>> On Thu, Nov 25, 2010 at 9:44 PM, Tsjerk Wassenaar <tsjerkw at gmail.com<mailto:
>> tsjerkw at gmail.com>> wrote:
>>
>>    Hey,
>>
>>    For this particular conversion you can also usually use 'mv':
>>
>>    mv file.pqr file.pdb
>>
>>    Btw, many of these file types are human readable. It usually helps
>>    quite a bit to look at the files and get acquainted with the file
>>    formats.
>>
>>    Cheers,
>>
>>    Tsjerk
>>
>>     On Nov 22, 2010 12:42 PM, "Mark Abraham" <Mark.Abraham at anu.edu.au
>>>    <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>>
>>>    On 22/11/2010 10:16 PM, mohsen ramezanpour wrote: > > Dear  All >
>>>    > I had a pdb file who was incompl...
>>>
>>>    Ask it for a pdb format. There should be no tool that builds atoms
>>>    that cannot write a standard file format like PDB - particularly
>>>    as PQR is a derivative of PDB.
>>>
>>>    Oh, and this is a bit off-topic for this list :-)
>>>
>>>    Mark
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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