AMBER Archive (2003)

Subject: AMBER: Any correct way to image a molecule ?

From: Teletchéa Stéphane (steletch_at_biomedicale.univ-paris5.fr)
Date: Thu Nov 13 2003 - 15:37:40 CST

I'm use to image my DNA strands with ptraj. The input file is generally
:
trajin dn300K1_c.gz
trajin dn300K2_c.gz
...
trajout dn300K.crd nobox
strip :CIP
strip :WAT
center origin
image center familiar
go

And it is able to bring back my two strands in the same box, so i can
visualise it correctly.

I'm now trying to find a way to do the same for the counter-ions and may
be some water molecules. But there, i'm encountering an imaging problem
: i've tried to be more precise in the centering, used masks, tried to
not remove conter-ions or even water (that makes a big trajectory).

I'm never getting one solely box, but at least what seems to be 4 or 8.

I've tried to change the size of the prmtop input file (the size of the
box is somehow diminished during the run : coming from 62/52/51 to
60/50/50), but now i'm not able to image the counter-ions.

I'm using ptraj from AMBER6, with suposedly all latest patches.

Any hint ?

Thank you in advance,
Regards,

Stéphane Teletchéa 

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