[gmx-users] two pdb files

[Tsjerk Wassenaar]

Hi,

Gromacs doesn't use residue numbers and atom numbers anyway. No
problem just concatenating a la Justin. If you still have to run
pdb2gmx, it may be better to have different chain identifiers. On tthe
other hand, it may be better to run pdb2gmx before concatenation
(which you probably have done already).

Cheers,

Tsjerk

On Wed, Oct 15, 2008 at 2:04 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Vitaly Chaban wrote:
>>
>> Hi Justin,
>>
>> The only problem of you way is that numbers in the resulting '.gro'
>> (after editconf -f *.pdb) file are wrong. But I still need it for the
>> calculation, of course.
>>
>
> The resulting .pdb will have to be modified slightly, as Florian noted.  You
> can then renumber it with genconf -renumber to get continuous numbering.
>
> If you need unique chain identifiers, that sort of thing could also be
> scripted if they are not already present.
>
> -Justin
>
>> Do you know any software to succeed with this task?
>> I tried to do it with MOLEKEL but (when I ask to save as PDB) it saves
>> only the first structure (from the first PDB file).
>>
>> Thanks, Vitaly
>>
>> JAL> Vitaly Chaban wrote:
>>>>
>>>> Hi,
>>>>
>>>> I have two pdb files of two equal boxes (with different particles in
>>>> them). I want just to concatenate them. I cannot do it with genbox
>>>> because it inserts only a part of one box into another. But the boxes
>>>> are absolutely equal. Thus, I need to insert box 'I' into box 'II'.
>>>> The boxes are made in such a way that the molecules don't intersect
>>>> after insertion.
>>>>
>>>> Does anybody know how to do it?
>>>>
>>
>> JAL> cat pdb1.pdb pdb2.pdb > pdb_both.pdb
>>
>> JAL> -Justin
>>
>>>> Or the same with .gro files?
>>>>
>>>> Thanks.
>>>>
>>>> Vitaly
>>>>
>>
>>
>
> --
> ========================================
>
> 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
F: +31-30-2537623