[gmx-users] two pdb files

Vitaly Chaban vvchaban at gmail.com
Wed Oct 15 14:03:13 CEST 2008

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.

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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