[gmx-users] .pqr to .pdb

[Justin A. Lemkul]

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.

> 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.

-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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-- 
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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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