Well,
sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'
file.pdb | sort | cut -b 2- > sorted.pdb
sort of seems to do the trick. But it will place the chainless things first.
Hope it helps,
Tsjerk
On Tue, Aug 12, 2008 at 3:13 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
>
> vivek sharma wrote:
>>
>> Hi david,
>> Thanx again, but I want to ask what changes need to be done there in such
>> cases.
>>
>
> The chain identifier needs to be continuous. That is, if you have atoms
> with chain identifiers like:
>
> A
> A
> B
> A
> C
> A
> A
>
> they should be re-written as:
>
> A
> A
> A
> A
> A
> B
> C
>
> This can be accomplished with some work in a simple text editor.
>
> -Justin
>
>> With Thanx,
>> Vivek
>>
>> 2008/8/12 David van der Spoel <[EMAIL PROTECTED]
>> <mailto:[EMAIL PROTECTED]>>
>>
>> vivek sharma wrote:
>>
>> Hi David,
>> Thanks for the quick reply. My apologies for asking you again a
>> silly doubt as, I am doing this all for the first time. It will
>> be of great help if you can tell me how to do such correction
>> manually.
>>
>>
>> with a text editor, like emacs, notepad or whatever.
>>
>>
>> With Thanx,
>> Vivek
>>
>> 2008/8/12 David van der Spoel <[EMAIL PROTECTED]
>> <mailto:[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED]
>> <mailto:[EMAIL PROTECTED]>>>
>>
>>
>> vivek sharma wrote:
>>
>> Hello there,
>> I am trying to run pdb2gmx on 3bzu.pdb file and got the
>> following error
>>
>> Opening library file /usr/share/gromacs/top/
>> ffG43b1.rtp
>> Opening library file /usr/share/gromacs/top/aminoacids.dat
>> Reading 3bzu.pdb...
>> WARNING: all CONECT records are ignored
>> Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6
>> BETA-HSD1', 8581 atoms
>> Opening library file /usr/share/gromacs/top/xlateat.dat
>> 26 out of 26 lines of xlateat.dat converted succesfully
>> Analyzing pdb file
>>
>> -------------------------------------------------------
>> Program pdb2gmx, VERSION 3.3.3
>> Source code file: pdb2gmx.c, line: 878
>>
>> Fatal error:
>> Chain identifier 'A' was used in two non-sequential blocks
>> (residue 1034, atom 7961)
>> -------------------------------------------------------
>> as I am new to this field. I'm finding it very difficult to
>> find the reason and rectify it.
>> Any suggestion would be of great help......
>>
>> This is a limitation in pdb2gmx. It expects the atoms in the
>> chain
>> A to be in sequence in the pdb file. You can manually sort
>> the pdb
>> file on the chain identifier.
>>
>>
>> With Thanx,
>> Vivek
>>
>> ------------------------------------------------------------------------
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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