[gmx-users] two pdb files

Vitaly Chaban vvchaban at gmail.com
Wed Oct 15 14:55:17 CEST 2008

Justin, Florian,
Thank you very much!

> genconf -renumber
Very useful feature! I do not know why it is not listed with
 genconf -h
 in my gmx-3.3.1 but it works.

>  and perhaps cahnge numbering.
Yes, the problem was in fact in quick changing numbers. I just used
cat 1.gro 2.gro > 12.gro
and then
genconf -f 12.gro -renumber.


JAL> 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.

JAL> The resulting .pdb will have to be modified slightly, as Florian noted.  You can
JAL> then renumber it with genconf -renumber to get continuous numbering.

JAL> If you need unique chain identifiers, that sort of thing could also be scripted
JAL> if they are not already present.

JAL> -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

Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban
tel.: +38-097-8259698

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