On 6/12/2007 7:15 PM, Miguel Machuqueiro wrote:
At 08:00 AM 6/12/2007, you wrote:
Hi again,
since I did not get answer I double checked my trr file. In case I
calculate the minimum distance of
the periodic image for each component of my complex, I get reasonable
value of it (3.0 and 2.9 nm),
whereas if I consider the whole system (protein) I get this strange
result of 0.17 nm.
Any clue?
thanks again
Regards
Hi Andrea,
When you have a multi-chain protein (or a protein + peptide) it can
happen that when making protein whole (removing pbc) sometimes the two
chains can be placed in two different adjacent boxes, so... when doing
the "g_mindist -pi" setup, the closest distance is when they are
together in the same box at a distance of ~1.7 Angstrom.
Point 1 - This is an artifact, but it doesn't exclude the possibility
that there are structures seeing their periodic images. As it was
suggested by Mark Abraham, you should check these structures just to
be sure.
Point 2 - If someone knows how to trick trjconv -pbc in order to avoid
doing this... it would be appreciated.
Yes. I got such "separated chain" trajectory with dsDNA as well. I have
a script to move them back manually frame per frame by comparing minimal
distance and real distance.
Miguel
========================================
Miguel Machuqueiro
ITQB-Instituto de Tecnologia Química e Biológica
Universidade Nova de Lisboa
Molecular Simulation Group - 6º Floor (Room 601)
Av. da República, EAN, Apartado 127
2781-901 Oeiras, Portugal
Tel. : +351 214469618 /Mobile: +351 96 7562285
E-mail: machuque at itqb.unl.pt
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